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Amelogenesis imperfecta v4.25 ALPL Claire Smith gene: ALPL was added
gene: ALPL was added to Amelogenesis imperfecta. Sources: Literature,Expert Review
Mode of inheritance for gene: ALPL was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Penetrance for gene: ALPL were set to Complete
Review for gene: ALPL was set to GREEN
Added comment: According to the review of ALPL literature, PMID: 39872235
"78.8% of adults with pediatric-onset HPP have dental involvement vs 42.6% of those with adult-onset HPP."
"clinical observations can include enamel hypoplasia and discoloration (possibly contributing to increased caries prevalence), delayed tooth eruption, tooth mobility, and malocclusion (misalignment of upper and lower teeth due to incorrect positions along the dental arches)"

(Note that enamel hypoplasia, although it can mean just specific teeth being affected, is also a term often used to reflect amelogenesis imperfecta in the presence of diseases affecting other organ systems, this is because the original definition of amelogenesis imperfecta excluded it being part of syndromic diseases, this is now changing)

According to Chavez et al.'s ALPL review PMID: 32758526
"Ameloblasts, odontoblasts, cementoblasts, osteoblasts, and periodontal ligament (PDL) cells express TNAP (encoded by ALPL) ( (Bowden and Foster, 2019, Zweifler et al., 2015), indicating the enzyme may function in all aspects of dental and periodontal mineralization."

ALPL is also included on the panel used by Fulgent genetics to screen patients with amelogenesis imperfecta
https://fulgentgenetics.com/Amelogenesis-Imperfecta
Sources: Literature, Expert Review
Amelogenesis imperfecta v4.16 TP63 Ida Ertmanska changed review comment from: Comment on list classification: Monoallelic variants may cause Ectrodactyly, ectodermal dysplasia, and cleft lip/palate syndrome 3 (OMIM:604292). At least 5 patients heterozygous for TP63 variants presented with dental abnormalities, as part of a syndromic presentation: missing teeth (3/5), enamel defects (3/5), taurodontia, peg-shaped teeth. However, the presentation in variable, and 2/5 variants showed incomplete penetrance (healthy heterozygous parents). Based on the available evidence, this gene is recommended for Green rating for Amelogenesis imperfecta, with an additional request of Expert Review.; to: Comment on list classification: Monoallelic variants may cause Ectrodactyly, ectodermal dysplasia, and cleft lip/palate syndrome 3 (OMIM:604292). At least 5 patients heterozygous for TP63 variants presented with dental abnormalities, as part of a syndromic presentation: missing teeth (3/5), enamel defects (3/5), taurodontia, peg-shaped teeth. However, the presentation in variable, and 2/5 variants showed incomplete penetrance (healthy heterozygous parents). The association is supported by a knockout mouse model, showing absence of hair follicles, teeth and mammary glands (PMID: 10227293). Based on the available evidence, this gene is recommended for Green rating for Amelogenesis imperfecta, with an additional request of Expert Review.
Amelogenesis imperfecta v4.12 TP63 Ida Ertmanska edited their review of gene: TP63: Added comment: Comment on list classification: Monoallelic variants may cause Ectrodactyly, ectodermal dysplasia, and cleft lip/palate syndrome 3 (OMIM:604292). At least 5 patients heterozygous for TP63 variants presented with dental abnormalities, as part of a syndromic presentation: missing teeth (3/5), enamel defects (3/5), taurodontia, peg-shaped teeth. However, the presentation in variable, and 2/5 variants showed incomplete penetrance (healthy heterozygous parents). Based on the available evidence, this gene is recommended for Green rating for Amelogenesis imperfecta, with an additional request of Expert Review.; Changed rating: GREEN
Amelogenesis imperfecta v4.12 TP63 Ida Ertmanska changed review comment from: PMID: 22065540 Kantaputra et al., 2012
Mother and son affected with split hand-split foot (formerly described as ectrodactyly), ectodermal dysplasia, hyperpigmentation of skin, and dystrophic nails. Heterozygous c.588-2A > C variant detected in TP63 in both mother and son. Only the son was affected with Amelogenesis Imperfecta (hypocalcification, hypoplasia, and hypomaturation), in the primary and permanent dentition. Mother had no dental abnormalities - incomplete penetrance?

PMID: 33126320 Otsuki et al., 2020
Case report: 13-year-old Japanese boy with ectrodactyly in the right hand and left foot and syndactyly in the left and right foot; skin abnormalities including dry skin and café au lait spots; teeth with peg-shaped appearance. Het for a maternally transmitted c.956G>A, p.(R319H) variant in TP63 - however, the mother was healthy.

PMID: 31050217 Zheng et al., 2021
Proband 1 - 6yo Chinese girl - Phenotype: nail dysplasia of the second toe; her hair was yellow when she was a baby; cutaneous syndactyly; missing distal phalanx of the second toe of the left foot; congenital lack of deciduous and permanent teeth, and taurodontia; remaining deciduous teeth in the mouth could be seen with enamel hypoplasia and caries. WES and Sanger results revealed a heterozygous TP63 mutation c.728G>A (p.R243Q). Father of the proband was similarly affected, and carried the same TP63 variant.
Proband 2 - 18‐year‐old Chinese boy - phenotype: sparse and curly hair, missing teeth; ectrodactyly on both hands and feet with dysplastic nails; heterozygous for a de novo c.955C>T (p.R319C) variant in TP63.
Proband 3 - 12‐year‐old Chinese boy - severe ectodermal phenotypes: lack of hair, sparse eyebrows, no eyelashes, underactive sweat glands, nail dysplasia, and missing teeth; short stature noted; Oral examination showed multiple congenitally missing permanent teeth. The remaining teeth displayed enamel hypoplasia and dentin exposure. Proband was heterozygous for c.1769C>T (p.P590L) in TP63 - de novo.

Functional evidence: complete deletion of mouse TP63 results in epidermal defects and epithelial abnormalities - including absence of hair follicles, teeth and mammary glands (PMID: 10227293 Mills et al., 1999).

This gene is associated with multiple autosomal dominant conditions in OMIM, including AD Ectrodactyly, ectodermal dysplasia, and cleft lip/palate syndrome 3, OMIM:604292 (accessed 7th Nov 2025).; to: PMID: 22065540 Kantaputra et al., 2012
Mother and son affected with split hand-split foot (formerly described as ectrodactyly), ectodermal dysplasia, hyperpigmentation of skin, and dystrophic nails. Heterozygous c.588-2A > C variant detected in TP63 in both mother and son. Only the son was affected with Amelogenesis Imperfecta (hypocalcification, hypoplasia, and hypomaturation), in the primary and permanent dentition. Mother had no dental abnormalities - incomplete penetrance?

PMID: 33126320 Otsuki et al., 2020
Case report: 13-year-old Japanese boy with ectrodactyly in the right hand and left foot and syndactyly in the left and right foot; skin abnormalities including dry skin and café au lait spots; teeth with peg-shaped appearance. Het for a maternally transmitted c.956G>A, p.(R319H) variant in TP63 - however, the mother was healthy.

PMID: 31050217 Zheng et al., 2021
Seq method: WES in probands and Sanger in family members.
Proband 1 - 6yo Chinese girl - Phenotype: nail dysplasia of the second toe; her hair was yellow when she was a baby; cutaneous syndactyly; missing distal phalanx of the second toe of the left foot; congenital lack of deciduous and permanent teeth, and taurodontia; remaining deciduous teeth in the mouth could be seen with enamel hypoplasia and caries. WES and Sanger results revealed a heterozygous TP63 mutation c.728G>A (p.R243Q). Father of the proband was similarly affected, and carried the same TP63 variant.
Proband 2 - 18‐year‐old Chinese boy - phenotype: sparse and curly hair, missing teeth; ectrodactyly on both hands and feet with dysplastic nails; heterozygous for a de novo c.955C>T (p.R319C) variant in TP63.
Proband 3 - 12‐year‐old Chinese boy - severe ectodermal phenotypes: lack of hair, sparse eyebrows, no eyelashes, underactive sweat glands, nail dysplasia, and missing teeth; short stature noted; Oral examination showed multiple congenitally missing permanent teeth. The remaining teeth displayed enamel hypoplasia and dentin exposure. Proband was heterozygous for c.1769C>T (p.P590L) in TP63 - de novo.

Functional evidence: complete deletion of mouse TP63 results in epidermal defects and epithelial abnormalities - including absence of hair follicles, teeth and mammary glands (PMID: 10227293 Mills et al., 1999).

This gene is associated with multiple autosomal dominant conditions in OMIM, including AD Ectrodactyly, ectodermal dysplasia, and cleft lip/palate syndrome 3, OMIM:604292 (accessed 7th Nov 2025).
Amelogenesis imperfecta v4.12 NECTIN4 Ida Ertmanska changed review comment from: Comment on list classification: there are at least 6 unrelated individuals with biallelic NECTIN4 variants and Ectodermal dysplasia-syndactyly syndrome 1. All affected individuals presented with dental abnormalities, including enamel hypoplasia, tooth agenesis, and peg-shaped, widely-spaced teeth. Based on available evidence, this gene should be promoted to Green for Amelogenesis imperfecta at the next GMS update.; to: Comment on list classification: There are at least 6 unrelated individuals with biallelic NECTIN4 variants and Ectodermal dysplasia-syndactyly syndrome 1. All affected individuals presented with dental abnormalities, including enamel hypoplasia, tooth agenesis, and peg-shaped, widely-spaced teeth. Based on available evidence, this gene should be promoted to Green for Amelogenesis imperfecta at the next GMS update.
Amelogenesis imperfecta v4.11 NECTIN4 Ida Ertmanska Phenotypes for gene: NECTIN4 were changed from syndactyly of the toes and fingers; hair abnormalities; variable dental genesis; enamel hypoplasia (amelogenesis imperfecta?); variable nail dystrophy; variable palmoplantar keratoderma, hyperkeratosis, reduced sweating to Ectodermal dysplasia-syndactyly syndrome 1, OMIM:613573; ectodermal dysplasia-syndactyly syndrome 1, MONDO:0024565; amelogenesis imperfecta, MONDO:0019507
Amelogenesis imperfecta v4.9 NECTIN4 Ida Ertmanska commented on gene: NECTIN4: Comment on list classification: there are at least 6 unrelated individuals with biallelic NECTIN4 variants and Ectodermal dysplasia-syndactyly syndrome 1. All affected individuals presented with dental abnormalities, including enamel hypoplasia, tooth agenesis, and peg-shaped, widely-spaced teeth. Based on available evidence, this gene should be promoted to Green for Amelogenesis imperfecta at the next GMS update.
Amelogenesis imperfecta v4.9 NECTIN4 Ida Ertmanska changed review comment from: PMID: 20691405 Brancati et al. 2010
Family A - 4 affected siblings, Algerian origins, first-cousin parents; c.851G>A (p.Arg284Gln), homozygous; phenotype: progressive alopecia, pili torti, widely-spaced peg-shaped teeth, syndactyly fingers 2-3/3-4, toes 2-3/4-5. Study shows that the variants results in exon 4 skipping, leading to a p.(Phe244CysfsX22) change (premature stop codon).
Family B - 2 sibs born to nonconsanguineous Italian parents; phenotype: alopecia, pili torti, abnormal teeth, cutaneous syndactyly. Compound heterozygous c.554C>T (p.Thr185Met) + c.906delT (p.Pro304HisfsX2). 50% reduced mRNA expression in cultured epidermal keratinocytes of patient II:1 (family B).

PMID: 21346770, Jelani et al. 2011
10 affected individuals across a consanguineous Pakistani pedigree. Used microsatellite markers to assign disease locus. Affected individuals homozygous for c.635C>G; p.Pro212Arg - LOD score 5.05. Phenotype: sparse hair, conical teeth with enamel hypoplasia, nail dystrophy, palmoplantar keratoderma, bilateral syndactyly fingers 3-4 and toes 2-3.

PMID: 34067522 Rotunno et al., 2021
Reports 5yo female patient; c.1150delC (p.Gln384ArgfsTer7), homozygous; phenotype: Brittle hair, sparse eyebrows/eyelashes, toenail dystrophy, mild palmoplantar keratoderma. Her teeth were widely spaced and conical, with small crowns and enamel hypoplasia + agenesis of 4 wisdom teeth.

PMID: 37829154 Ali et al., 2023
Consanguineous Kashmiri Family. All 4 affected individuals harboured a homozygous nonsense variant NM 030916: c.181C > T, p.(Gln61Ter). Method: WES. Hypotrichosis, syndactyly fingers 3-4 and toes 2-3, discolored nails, upper lip cleft; conical teeth, with enamel ridges, and pits, widely spaced.

PMID: 37183149 Hajra et al., 2023
Large consanguineous Pakistani family. Only NECTIN4 coding region sequenced. All 15 affected individuals were homozygous for c.163C>T; p.(Arg55*). Phenotype: sparse hair; hypoplastic nails with thick flat discoloured nail plates; peg-shaped, conical, and widely spaced teeth with enamel hypoplasia; proximal cutaneous syndactyly of fingers and toes; skin was dry and scaly with hyperkeratosis and palmoplantar keratoderma.
;
PMID: 40586252 Abu Assab et al. 2025; to: PMID: 20691405 Brancati et al. 2010
Family A - 4 affected siblings, Algerian origins, first-cousin parents; c.851G>A (p.Arg284Gln), homozygous; phenotype: progressive alopecia, pili torti, widely-spaced peg-shaped teeth, syndactyly fingers 2-3/3-4, toes 2-3/4-5. Study shows that the variants results in exon 4 skipping, leading to a p.(Phe244CysfsX22) change (premature stop codon).
Family B - 2 sibs born to nonconsanguineous Italian parents; phenotype: alopecia, pili torti, abnormal teeth, cutaneous syndactyly. Compound heterozygous c.554C>T (p.Thr185Met) + c.906delT (p.Pro304HisfsX2). 50% reduced mRNA expression in cultured epidermal keratinocytes of patient II:1 (family B).

PMID: 21346770, Jelani et al. 2011
10 affected individuals across a consanguineous Pakistani pedigree. Used microsatellite markers to assign disease locus. Affected individuals homozygous for c.635C>G; p.Pro212Arg - LOD score 5.05. Phenotype: sparse hair, conical teeth with enamel hypoplasia, nail dystrophy, palmoplantar keratoderma, bilateral syndactyly fingers 3-4 and toes 2-3.

PMID: 34067522 Rotunno et al., 2021
Reports 5yo female patient; c.1150delC (p.Gln384ArgfsTer7), homozygous; phenotype: Brittle hair, sparse eyebrows/eyelashes, toenail dystrophy, mild palmoplantar keratoderma. Her teeth were widely spaced and conical, with small crowns and enamel hypoplasia + agenesis of 4 wisdom teeth.

PMID: 37829154 Ali et al., 2023
Consanguineous Kashmiri Family. All 4 affected individuals harboured a homozygous nonsense variant NM 030916: c.181C > T, p.(Gln61Ter). Method: WES. Hypotrichosis, syndactyly fingers 3-4 and toes 2-3, discolored nails, upper lip cleft; conical teeth, with enamel ridges, and pits, widely spaced.

PMID: 37183149 Hajra et al., 2023
Large consanguineous Pakistani family. Only NECTIN4 coding region sequenced. All 15 affected individuals were homozygous for c.163C>T; p.(Arg55*). Phenotype: sparse hair; hypoplastic nails with thick flat discoloured nail plates; peg-shaped, conical, and widely spaced teeth with enamel hypoplasia; proximal cutaneous syndactyly of fingers and toes; skin was dry and scaly with hyperkeratosis and palmoplantar keratoderma.

NECTIN4, previously known as PVRL4, is linked to Ectodermal dysplasia-syndactyly syndrome 1, 613573 (OMIM, accessed 7th Nov 2025).
Amelogenesis imperfecta v4.9 CLDN16 Ida Ertmanska changed review comment from: Comment on list classification: There are 6 unrelated individuals reported in literature with biallelic variants in CLDN16 with amelogenesis imperfecta. The enamel defects are part of a syndromic presentation of familial hypomagnesemia with hypercalciuria and nephrocalcinosis. The association is supported by a Cldn16−/− mouse model, showing enamel fractures and coronal dentin exposition on molars, caused by ameloblast defects and low extracellular pH. Based on the available evidence, this gene should be promoted to Green for Amelogenesis imperfecta at the next GMS update.; to: Comment on list classification: There are 6 unrelated individuals reported in literature with biallelic variants in CLDN16 with amelogenesis imperfecta. The dental defects are part of a syndromic presentation of familial hypomagnesemia with hypercalciuria and nephrocalcinosis. The association is supported by a Cldn16−/− mouse model, showing enamel fractures and coronal dentin exposition on molars, caused by ameloblast defects and low extracellular pH. Based on the available evidence, this gene should be promoted to Green for Amelogenesis imperfecta at the next GMS update.
Amelogenesis imperfecta v4.9 CLDN16 Ida Ertmanska changed review comment from: Comment on list classification: There are at 6 unrelated individuals reported in literature with biallelic variants in CLDN16 with amelogenesis imperfecta. The enamel defects are part of a syndromic presentation of familial hypomagnesemia with hypercalciuria and nephrocalcinosis. The association is supported by a Cldn16−/− mouse model, showing enamel fractures and coronal dentin exposition on molars, caused by ameloblast defects and low extracellular pH. Based on the available evidence, this gene should be promoted to Green for Amelogenesis imperfecta at the next GMS update.; to: Comment on list classification: There are 6 unrelated individuals reported in literature with biallelic variants in CLDN16 with amelogenesis imperfecta. The enamel defects are part of a syndromic presentation of familial hypomagnesemia with hypercalciuria and nephrocalcinosis. The association is supported by a Cldn16−/− mouse model, showing enamel fractures and coronal dentin exposition on molars, caused by ameloblast defects and low extracellular pH. Based on the available evidence, this gene should be promoted to Green for Amelogenesis imperfecta at the next GMS update.
Amelogenesis imperfecta v4.9 CLDN16 Ida Ertmanska commented on gene: CLDN16: Comment on list classification: There are at 6 unrelated individuals reported in literature with biallelic variants in CLDN16 with amelogenesis imperfecta. The enamel defects are part of a syndromic presentation of familial hypomagnesemia with hypercalciuria and nephrocalcinosis. The association is supported by a Cldn16−/− mouse model, showing enamel fractures and coronal dentin exposition on molars, caused by ameloblast defects and low extracellular pH. Based on the available evidence, this gene should be promoted to Green for Amelogenesis imperfecta at the next GMS update.
Amelogenesis imperfecta v4.9 AIRE Ida Ertmanska changed review comment from: PMID 19393987 Pavlic and Waltimo-Sirén, 2009
Patients with autoimmune polyendocrinopathy–candidiasis–ectodermal dystrophy (APECED), also known as autoimmune polyglandular syndrome type I (APS 1).
Family 1 - female patient A, 9yo, oldest child of three siblings - compound heterozygote with R257X / 653-7_-5delCTC mutations in AIRE. Presented with hypoplastic enamel, hypoparathyroidism (HPT), hypoadrenocorticism, and chronic mucocutaneous candidiasis (CMC). Siblings asymptomatic, not genotyped.
Family 2 - female proband (patient B) with APECED harboured compound het mutations in AIRE: p.Arg257Ter; p.Thr16Met. Unaffected family members were either carriers or WT. Similarly affected brother (patient C), who harboured the same variants in AIRE.
Patient B presented with ectodermal dystrophy and HPT at age 5, and CMC at age 11. Panoramic tomogram at age 11 showed markedly thin and uneven enamel; premolars erupted with discoloured and hypoplastic enamel; she needed prosthetic crowns for her premolars before age 15; moderate to severe tooth sensitivity.

PMID: 27253668 Bruserud et al., 2016
Report of fifty-two patients from 34 Norwegian families with biallelic variants in AIRE. Enamel hypoplasia, hypoparathyroidism, and CMC were the most frequent components. Of 25 patients examined by a dentist, 18 presented with enamel hypoplasia (72%), onset mostly in adolescence.

PMID: 31905445 Suh et al., 2019
10yo female Korean patient; compound het for c.1513delG (p.Ala505ProfsTer16) and c.1360dupC (p.His454ProfsTer50); presented with Primary adrenal insufficiency, Chronic mucocutaneous candidiasis (since 6 months of age), Dental enamel dysplasia, Hyperpigmentation.

PMID: 35521792 Cranston et al., 2022
Patient 15: age 19 at time of report, compound het. variants c.769C>T, p.(Arg257Ter); c.967_979del13, p.(Leu323fs) in AIRE. Presented with hypoparathyroidism, nail dystrophy, enamel hypoplasia, alopecia, tubulointerstitial nephritis.
Patient 19: onset at age 6, homozygous for c.967_979del13, p.(Leu323fs) - Mutation associated with uniparental isodisomy. Phenotype: hypoparathyroidism, enamel hypoplasia, and adrenal insufficiency.
In this cohort, 7% of mutation positive individuals, and 3% of mutation negative probands, presented with enamel hypoplasia. Ethnic background not disclosed.

Functional evidence:
PMID: 37993717 Gruper et al., 2023
Enamel defects similar to APS1 presentation develop in 20-50% of children with coeliac disease. Study shows that both APS1 and coeliac disease patients develop autoantibodies (mostly IgA isotype) against ameloblast specific proteins, leading to defects in enamel formation.
AIRE-deficient (-/-) mice have defective enamel formation; the KO mice showed autoreactivity to ameloblast antigens (slot-blot immunoassay).

Only 1 patient reported with a heterozygous variant in AIRE with enamel hypoplasia:
PMID: 37235056 Oftedal et al., 2023
Family X (II-I) - Female, USA - c.1102C>G, p.Pro368Ala - heterozygous variant, present in 14 individuals in gnomAD v4 (het only); Revel score = 0.27 Benign Supporting. Presented with migraines, chronic constipation, poor appetite, recurrent fever, proteinuria, hypoparathyroidism, enamel hypoplasia; positive for autoantibodies against IL-17A. Seq method: WES.
10 other patients with heterozygous variants in AIRE and APS1 did not present with enamel hypoplasia. Authors highlight incomplete penetrance of the dominant-negative mutations reported.

AIRE is linked to AR & AD Autoimmune polyendocrinopathy syndrome , type I, with or without reversible metaphyseal dysplasia, 240300 (OMIM, accessed 5th Nov 2025).; to: PMID 19393987 Pavlic and Waltimo-Sirén, 2009
Patients with autoimmune polyendocrinopathy–candidiasis–ectodermal dystrophy (APECED), also known as autoimmune polyglandular syndrome type I (APS 1).
Family 1 - female patient A, 9yo, oldest child of three siblings - compound heterozygote with R257X / 653-7_-5delCTC mutations in AIRE. Presented with hypoplastic enamel, hypoparathyroidism (HPT), hypoadrenocorticism, and chronic mucocutaneous candidiasis (CMC). Siblings asymptomatic, not genotyped.
Family 2 - female proband (patient B) with APECED harboured compound het mutations in AIRE: p.Arg257Ter; p.Thr16Met. Unaffected family members were either carriers or WT. Similarly affected brother (patient C), who harboured the same variants in AIRE.
Patient B presented with ectodermal dystrophy and HPT at age 5, and CMC at age 11. Panoramic tomogram at age 11 showed markedly thin and uneven enamel; premolars erupted with discoloured and hypoplastic enamel; she needed prosthetic crowns for her premolars before age 15; moderate to severe tooth sensitivity.

PMID: 27253668 Bruserud et al., 2016
Report of fifty-two patients from 34 Norwegian families with biallelic variants in AIRE (relatedness?). Enamel hypoplasia, hypoparathyroidism, and CMC were the most frequent components. Of 25 patients examined by a dentist, 18 presented with enamel hypoplasia (72%), onset mostly in adolescence.

PMID: 31905445 Suh et al., 2019
10yo female Korean patient; compound het for c.1513delG (p.Ala505ProfsTer16) and c.1360dupC (p.His454ProfsTer50); presented with Primary adrenal insufficiency, Chronic mucocutaneous candidiasis (since 6 months of age), Dental enamel dysplasia, Hyperpigmentation.

PMID: 35521792 Cranston et al., 2022
Patient 15: age 19 at time of report, compound het. variants c.769C>T, p.(Arg257Ter); c.967_979del13, p.(Leu323fs) in AIRE. Presented with hypoparathyroidism, nail dystrophy, enamel hypoplasia, alopecia, tubulointerstitial nephritis.
Patient 19: onset at age 6, homozygous for c.967_979del13, p.(Leu323fs) - Mutation associated with uniparental isodisomy. Phenotype: hypoparathyroidism, enamel hypoplasia, and adrenal insufficiency.
In this cohort, 7% of mutation positive individuals, and 3% of mutation negative probands, presented with enamel hypoplasia. Ethnic background not disclosed.

Functional evidence:
PMID: 37993717 Gruper et al., 2023
Enamel defects similar to APS1 presentation develop in 20-50% of children with coeliac disease. Study shows that both APS1 and coeliac disease patients develop autoantibodies (mostly IgA isotype) against ameloblast specific proteins, leading to defects in enamel formation.
AIRE-deficient (-/-) mice have defective enamel formation; the KO mice showed autoreactivity to ameloblast antigens (slot-blot immunoassay).

Only 1 patient reported with a heterozygous variant in AIRE with enamel hypoplasia:
PMID: 37235056 Oftedal et al., 2023
Family X (II-I) - Female, USA - c.1102C>G, p.Pro368Ala - heterozygous variant, present in 14 individuals in gnomAD v4 (het only); Revel score = 0.27 Benign Supporting. Presented with migraines, chronic constipation, poor appetite, recurrent fever, proteinuria, hypoparathyroidism, enamel hypoplasia; positive for autoantibodies against IL-17A. Seq method: WES.
10 other patients with heterozygous variants in AIRE and APS1 did not present with enamel hypoplasia. Authors highlight incomplete penetrance of the dominant-negative mutations reported.

AIRE is linked to AR & AD Autoimmune polyendocrinopathy syndrome , type I, with or without reversible metaphyseal dysplasia, 240300 (OMIM, accessed 5th Nov 2025).
Amelogenesis imperfecta v4.9 AIRE Ida Ertmanska changed review comment from: Comment on list classification: There are at least 23 patients reported in literature with biallelic variants in AIRE, diagnosed with APS-1 and presenting with marked enamel hypoplasia (onset mostly in childhood / adolescence). Only one APS-1 patient heterozygous for an AIRE variant presented with enamel hypoplasia. In addition, AIRE knock-out mice showed defective enamel formation (PMID: 37993717). Based on the available evidence, this gene should be rated Green for Amelogenesis imperfecta, with MOI set to BIALLELIC, autosomal or pseudoautosomal.; to: Comment on list classification: There are at least 5 patients reported in literature with biallelic variants in AIRE, diagnosed with APS-1 and presenting with marked enamel hypoplasia (onset mostly in childhood / adolescence). Only one APS-1 patient heterozygous for an AIRE variant presented with enamel hypoplasia. In addition, AIRE knock-out mice showed defective enamel formation (PMID: 37993717). Based on the available evidence, this gene should be rated Green for Amelogenesis imperfecta, with MOI set to BIALLELIC, autosomal or pseudoautosomal.
Amelogenesis imperfecta v4.9 AIRE Ida Ertmanska changed review comment from: Comment on list classification: There are at least 5 patients reported in literature with biallelic variants in AIRE, diagnosed with APS-1 and presenting with marked enamel hypoplasia (onset mostly in childhood / adolescence). Only one APS-1 patient heterozygous for an AIRE variant presented with enamel hypoplasia. In addition, AIRE knock-out mice showed defective enamel formation (PMID: 37993717). Based on the available evidence, this gene should be rated Green for Amelogenesis imperfecta, with MOI set to BIALLELIC, autosomal or pseudoautosomal.; to: Comment on list classification: There are at least 23 patients reported in literature with biallelic variants in AIRE, diagnosed with APS-1 and presenting with marked enamel hypoplasia (onset mostly in childhood / adolescence). Only one APS-1 patient heterozygous for an AIRE variant presented with enamel hypoplasia. In addition, AIRE knock-out mice showed defective enamel formation (PMID: 37993717). Based on the available evidence, this gene should be rated Green for Amelogenesis imperfecta, with MOI set to BIALLELIC, autosomal or pseudoautosomal.
Amelogenesis imperfecta v4.9 AIRE Ida Ertmanska changed review comment from: Comment on list classification: There are at least 23 patients reported in literature with biallelic variants in AIRE, diagnosed with APS 1 and presenting with marked enamel hypoplasia (onset mostly in childhood / adolescence). Only one APS-1 patient heterozygous for an AIRE variant presented with enamel hypoplasia. In addition, AIRE knock-out mice showed defective enamel formation (PMID: 37993717). Based on the available evidence, this gene should be rated Green for Amelogenesis imperfecta, with MOI set to BIALLELIC, autosomal or pseudoautosomal.; to: Comment on list classification: There are at least 5 patients reported in literature with biallelic variants in AIRE, diagnosed with APS-1 and presenting with marked enamel hypoplasia (onset mostly in childhood / adolescence). Only one APS-1 patient heterozygous for an AIRE variant presented with enamel hypoplasia. In addition, AIRE knock-out mice showed defective enamel formation (PMID: 37993717). Based on the available evidence, this gene should be rated Green for Amelogenesis imperfecta, with MOI set to BIALLELIC, autosomal or pseudoautosomal.
Amelogenesis imperfecta v4.9 AIRE Ida Ertmanska changed review comment from: Comment on list classification: There are at least 23 patients reported in literature with biallelic variants in AIRE, diagnosed with APS 1 and presenting with marked enamel hypoplasia (onset mostly in childhood / adolescence). Only one APS-1 patient heterozygous for an AIRE variant presented with enamel hypoplasia. Based on the available evidence, this gene should be rated Green for Amelogenesis imperfecta, with MOI set to BIALLELIC, autosomal or pseudoautosomal.; to: Comment on list classification: There are at least 23 patients reported in literature with biallelic variants in AIRE, diagnosed with APS 1 and presenting with marked enamel hypoplasia (onset mostly in childhood / adolescence). Only one APS-1 patient heterozygous for an AIRE variant presented with enamel hypoplasia. In addition, AIRE knock-out mice showed defective enamel formation (PMID: 37993717). Based on the available evidence, this gene should be rated Green for Amelogenesis imperfecta, with MOI set to BIALLELIC, autosomal or pseudoautosomal.
Amelogenesis imperfecta v4.9 AIRE Ida Ertmanska changed review comment from: Comment on list classification: There are at least 23 patients reported in literature with biallelic variants in AIRE, diagnosed with APS 1 and presenting with marked enamel hypoplasia (onset mostly in childhood / adolescence). Only 1 APS-1 patient heterozygous for an AIRE variant presented with enamel hypoplasia. Based on the available evidence, this gene should be rated Green for Amelogenesis imperfecta, with MOI set to BIALLELIC, autosomal or pseudoautosomal.; to: Comment on list classification: There are at least 23 patients reported in literature with biallelic variants in AIRE, diagnosed with APS 1 and presenting with marked enamel hypoplasia (onset mostly in childhood / adolescence). Only one APS-1 patient heterozygous for an AIRE variant presented with enamel hypoplasia. Based on the available evidence, this gene should be rated Green for Amelogenesis imperfecta, with MOI set to BIALLELIC, autosomal or pseudoautosomal.
Amelogenesis imperfecta v4.5 AIRE Ida Ertmanska commented on gene: AIRE: Comment on list classification: There are at least 23 patients reported in literature with biallelic variants in AIRE, diagnosed with APS 1 and presenting with marked enamel hypoplasia (onset mostly in childhood / adolescence). Only 1 APS-1 patient heterozygous for an AIRE variant presented with enamel hypoplasia. Based on the available evidence, this gene should be rated Green for Amelogenesis imperfecta, with MOI set to BIALLELIC, autosomal or pseudoautosomal.
Amelogenesis imperfecta v4.5 AIRE Ida Ertmanska changed review comment from: PMID 19393987 Pavlic and Waltimo-Sirén, 2009
Patients with autoimmune polyendocrinopathy–candidiasis–ectodermal dystrophy (APECED), also known as autoimmune polyglandular syndrome type I (APS 1).
Family 1 - female patient A, 9yo, oldest child of three siblings - compound heterozygote with R257X / 653-7_-5delCTC mutations in AIRE. Presented with hypoplastic enamel, hypoparathyroidism (HPT), hypoadrenocorticism, and chronic mucocutaneous candidiasis (CMC). Siblings asymptomatic, not genotyped.
Family 2 - female proband (patient B) with APECED harboured compound het mutations in AIRE: R257X/T16M. Unaffected family members were either carriers or WT. Similarly affected brother (patient C), who harboured the same variants in AIRE.
Patient B presented with ectodermal dystrophy and HPT at age 5, and CMC at age 11. Panoramic tomogram at age 11 showed markedly thin and uneven enamel; premolars erupted with discoloured and hypoplastic enamel; she needed prosthetic crowns for her premolars before age 15; moderate to severe tooth sensitivity.

PMID: 27253668 Bruserud et al., 2016
Report of fifty-two patients from 34 Norwegian families with biallelic variants in AIRE. Enamel hypoplasia, hypoparathyroidism, and CMC were the most frequent components. Of 25 patients examined by a dentist, 18 presented with enamel hypoplasia (72%), onset mostly in adolescence.

PMID: 31905445 Suh et al., 2019
10yo female Korean patient; compound het for c.1513delG (p.Ala505ProfsTer16) and c.1360dupC (p.His454ProfsTer50); presented with Primary adrenal insufficiency, Chronic mucocutaneous candidiasis (since 6 months of age), Dental enamel dysplasia, Hyperpigmentation.

PMID: 35521792 Cranston et al., 2022
Patient 15: age 19 at time of report, compound het. variants c.769C>T, p.(Arg257Ter); c.967_979del13, p.(Leu323fs) in AIRE. Presented with hypoparathyroidism, nail dystrophy, enamel hypoplasia, alopecia, tubulointerstitial nephritis.
Patient 19: onset at age 6, homozygous for c.967_979del13, p.(Leu323fs) - Mutation associated with uniparental isodisomy. Phenotype: hypoparathyroidism, enamel hypoplasia, and adrenal insufficiency.

Functional evidence:
PMID: 37993717 Gruper et al., 2023
Enamel defects similar to APS1 presentation develop in 20-50% of children with coeliac disease. Study shows that both APS1 and coeliac disease patients develop autoantibodies (mostly IgA isotype) against ameloblast specific proteins, leading to defects in enamel formation.
AIRE-deficient (-/-) mice have defective enamel formation; the KO mice showed autoreactivity to ameloblast antigens (slot-blot immunoassay).

Only 1 patient reported with a heterozygous variant in AIRE with enamel hypoplasia:
PMID: 37235056 Oftedal et al., 2023
Family X (II-I) - Female, USA - c.1102C>G, p.Pro368Ala - heterozygous variant, present in 14 individuals in gnomAD v4 (het only); Revel score = 0.27 Benign Supporting. Presented with migraines, chronic constipation, poor appetite, recurrent fever, proteinuria, hypoparathyroidism, enamel hypoplasia; positive for autoantibodies against IL-17A. Seq method: WES.
10 other patients with heterozygous variants in AIRE and APS1 did not present with enamel hypoplasia. Authors highlight incomplete penetrance of the dominant-negative mutations reported.; to: PMID 19393987 Pavlic and Waltimo-Sirén, 2009
Patients with autoimmune polyendocrinopathy–candidiasis–ectodermal dystrophy (APECED), also known as autoimmune polyglandular syndrome type I (APS 1).
Family 1 - female patient A, 9yo, oldest child of three siblings - compound heterozygote with R257X / 653-7_-5delCTC mutations in AIRE. Presented with hypoplastic enamel, hypoparathyroidism (HPT), hypoadrenocorticism, and chronic mucocutaneous candidiasis (CMC). Siblings asymptomatic, not genotyped.
Family 2 - female proband (patient B) with APECED harboured compound het mutations in AIRE: p.Arg257Ter; p.Thr16Met. Unaffected family members were either carriers or WT. Similarly affected brother (patient C), who harboured the same variants in AIRE.
Patient B presented with ectodermal dystrophy and HPT at age 5, and CMC at age 11. Panoramic tomogram at age 11 showed markedly thin and uneven enamel; premolars erupted with discoloured and hypoplastic enamel; she needed prosthetic crowns for her premolars before age 15; moderate to severe tooth sensitivity.

PMID: 27253668 Bruserud et al., 2016
Report of fifty-two patients from 34 Norwegian families with biallelic variants in AIRE. Enamel hypoplasia, hypoparathyroidism, and CMC were the most frequent components. Of 25 patients examined by a dentist, 18 presented with enamel hypoplasia (72%), onset mostly in adolescence.

PMID: 31905445 Suh et al., 2019
10yo female Korean patient; compound het for c.1513delG (p.Ala505ProfsTer16) and c.1360dupC (p.His454ProfsTer50); presented with Primary adrenal insufficiency, Chronic mucocutaneous candidiasis (since 6 months of age), Dental enamel dysplasia, Hyperpigmentation.

PMID: 35521792 Cranston et al., 2022
Patient 15: age 19 at time of report, compound het. variants c.769C>T, p.(Arg257Ter); c.967_979del13, p.(Leu323fs) in AIRE. Presented with hypoparathyroidism, nail dystrophy, enamel hypoplasia, alopecia, tubulointerstitial nephritis.
Patient 19: onset at age 6, homozygous for c.967_979del13, p.(Leu323fs) - Mutation associated with uniparental isodisomy. Phenotype: hypoparathyroidism, enamel hypoplasia, and adrenal insufficiency.
In this cohort, 7% of mutation positive individuals, and 3% of mutation negative probands, presented with enamel hypoplasia. Ethnic background not disclosed.

Functional evidence:
PMID: 37993717 Gruper et al., 2023
Enamel defects similar to APS1 presentation develop in 20-50% of children with coeliac disease. Study shows that both APS1 and coeliac disease patients develop autoantibodies (mostly IgA isotype) against ameloblast specific proteins, leading to defects in enamel formation.
AIRE-deficient (-/-) mice have defective enamel formation; the KO mice showed autoreactivity to ameloblast antigens (slot-blot immunoassay).

Only 1 patient reported with a heterozygous variant in AIRE with enamel hypoplasia:
PMID: 37235056 Oftedal et al., 2023
Family X (II-I) - Female, USA - c.1102C>G, p.Pro368Ala - heterozygous variant, present in 14 individuals in gnomAD v4 (het only); Revel score = 0.27 Benign Supporting. Presented with migraines, chronic constipation, poor appetite, recurrent fever, proteinuria, hypoparathyroidism, enamel hypoplasia; positive for autoantibodies against IL-17A. Seq method: WES.
10 other patients with heterozygous variants in AIRE and APS1 did not present with enamel hypoplasia. Authors highlight incomplete penetrance of the dominant-negative mutations reported.

AIRE is linked to AR & AD Autoimmune polyendocrinopathy syndrome , type I, with or without reversible metaphyseal dysplasia, 240300 (OMIM, accessed 5th Nov 2025).
Amelogenesis imperfecta v4.5 AIRE Ida Ertmanska changed review comment from: PMID 19393987 Pavlic and Waltimo-Sirén, 2009
Patients with autoimmune polyendocrinopathy–candidiasis–ectodermal dystrophy (APECED), also known as autoimmune polyglandular syndrome type I (APS 1).
Family 1 - female patient A, 9yo, oldest child of three siblings - compound heterozygote with R257X / 653-7_-5delCTC mutations in AIRE. Presented with hypoplastic enamel, hypoparathyroidism (HPT), hypoadrenocorticism, and chronic mucocutaneous candidiasis (CMC). Siblings asymptomatic, not genotyped.
Family 2 - female proband (patient B) with APECED harboured compound het mutations in AIRE: R257X/T16M. Unaffected family members were either carriers or WT. Similarly affected brother (patient C), who harboured the same variants in AIRE.
Patient B presented with ectodermal dystrophy and HPT at age 5, and CMC at age 11. Panoramic tomogram at age 11 showed markedly thin and uneven enamel; premolars erupted with discoloured and hypoplastic enamel; she needed prosthetic crowns for her premolars before age 15; moderate to severe tooth sensitivity.

PMID: 27253668 Bruserud et al., 2016
Report of fifty-two patients from 34 Norwegian families with biallelic variants in AIRE. Enamel hypoplasia, hypoparathyroidism, and CMC were the most frequent components. Of 25 patients examined by a dentist, 18 presented with enamel hypoplasia (72%), onset mostly in adolescence.

PMID: 31905445 Suh et al., 2019
10yo female Korean patient; compound het for c.1513delG (p.Ala505ProfsTer16) and c.1360dupC (p.His454ProfsTer50); presented with Primary adrenal insufficiency, Chronic mucocutaneous candidiasis (since 6 months of age), Dental enamel dysplasia, Hyperpigmentation.

PMID: 35521792 Cranston et al., 2022
Patient 15: age 19 at time of report, compound het. variants c.769C>T, p.(Arg257Ter); c.967_979del13, p.(Leu323fs) in AIRE. Presented with hypoparathyroidism, nail dystrophy, enamel hypoplasia, alopecia, tubulointerstitial nephritis.
Patient 19: onset at age 6, homozygous for c.967_979del13, p.(Leu323fs) - Mutation associated with uniparental isodisomy. Phenotype: hypoparathyroidism, enamel hypoplasia, and adrenal insufficiency.

Functional evidence:
PMID: 37993717 Gruper et al., 2023
Enamel defects similar to APS1 presentation develop in 20-50% of children with coeliac disease. Study shows that both APS1 and coeliac disease patients develop autoantibodies (mostly IgA isotype) against ameloblast specific proteins, leading to defects in enamel formation.
AIRE-deficient (-/-) mice have defective enamel formation; the KO mice showed autoreactivity to ameloblast antigens (slot-blot immunoassay).

Only 1 patient reported with a heterozygous variant in AIRE with enamel hypoplasia:
PMID: 37235056 Oftedal et al., 2023
Family X (II-I) - Female, USA - c.1102C>G, p.Pro368Ala - heterozygous variant, present in 14 individuals in gnomAD v4 (het only); Revel score = 0.27 Benign Supporting. Presented with migraines, chronic constipation, poor appetite, recurrent fever, proteinuria, hypoparathyroidism, enamel hypoplasia; positive for autoantibodies against IL-17A. Seq method: WES.
10 other patients with heterozygous variants in AIRE and APS1 did not present with enamel hypoplasia. Authors highlight incomplete penetrance of the dominant-negative mutations reported.; to: PMID 19393987 Pavlic and Waltimo-Sirén, 2009
Patients with autoimmune polyendocrinopathy–candidiasis–ectodermal dystrophy (APECED), also known as autoimmune polyglandular syndrome type I (APS 1).
Family 1 - female patient A, 9yo, oldest child of three siblings - compound heterozygote with R257X / 653-7_-5delCTC mutations in AIRE. Presented with hypoplastic enamel, hypoparathyroidism (HPT), hypoadrenocorticism, and chronic mucocutaneous candidiasis (CMC). Siblings asymptomatic, not genotyped.
Family 2 - female proband (patient B) with APECED harboured compound het mutations in AIRE: R257X/T16M. Unaffected family members were either carriers or WT. Similarly affected brother (patient C), who harboured the same variants in AIRE.
Patient B presented with ectodermal dystrophy and HPT at age 5, and CMC at age 11. Panoramic tomogram at age 11 showed markedly thin and uneven enamel; premolars erupted with discoloured and hypoplastic enamel; she needed prosthetic crowns for her premolars before age 15; moderate to severe tooth sensitivity.

PMID: 27253668 Bruserud et al., 2016
Report of fifty-two patients from 34 Norwegian families with biallelic variants in AIRE. Enamel hypoplasia, hypoparathyroidism, and CMC were the most frequent components. Of 25 patients examined by a dentist, 18 presented with enamel hypoplasia (72%), onset mostly in adolescence.

PMID: 31905445 Suh et al., 2019
10yo female Korean patient; compound het for c.1513delG (p.Ala505ProfsTer16) and c.1360dupC (p.His454ProfsTer50); presented with Primary adrenal insufficiency, Chronic mucocutaneous candidiasis (since 6 months of age), Dental enamel dysplasia, Hyperpigmentation.

PMID: 35521792 Cranston et al., 2022
Patient 15: age 19 at time of report, compound het. variants c.769C>T, p.(Arg257Ter); c.967_979del13, p.(Leu323fs) in AIRE. Presented with hypoparathyroidism, nail dystrophy, enamel hypoplasia, alopecia, tubulointerstitial nephritis.
Patient 19: onset at age 6, homozygous for c.967_979del13, p.(Leu323fs) - Mutation associated with uniparental isodisomy. Phenotype: hypoparathyroidism, enamel hypoplasia, and adrenal insufficiency.

Functional evidence:
PMID: 37993717 Gruper et al., 2023
Enamel defects similar to APS1 presentation develop in 20-50% of children with coeliac disease. Study shows that both APS1 and coeliac disease patients develop autoantibodies (mostly IgA isotype) against ameloblast specific proteins, leading to defects in enamel formation.
AIRE-deficient (-/-) mice have defective enamel formation; the KO mice showed autoreactivity to ameloblast antigens (slot-blot immunoassay).

Only 1 patient reported with a heterozygous variant in AIRE with enamel hypoplasia:
PMID: 37235056 Oftedal et al., 2023
Family X (II-I) - Female, USA - c.1102C>G, p.Pro368Ala - heterozygous variant, present in 14 individuals in gnomAD v4 (het only); Revel score = 0.27 Benign Supporting. Presented with migraines, chronic constipation, poor appetite, recurrent fever, proteinuria, hypoparathyroidism, enamel hypoplasia; positive for autoantibodies against IL-17A. Seq method: WES.
10 other patients with heterozygous variants in AIRE and APS1 did not present with enamel hypoplasia. Authors highlight incomplete penetrance of the dominant-negative mutations reported.
Amelogenesis imperfecta v4.5 NECTIN4 Claire Smith gene: NECTIN4 was added
gene: NECTIN4 was added to Amelogenesis imperfecta. Sources: Literature
Mode of inheritance for gene: NECTIN4 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: NECTIN4 were set to PMID: 34067522; 37183149
Phenotypes for gene: NECTIN4 were set to syndactyly of the toes and fingers; hair abnormalities; variable dental genesis; enamel hypoplasia (amelogenesis imperfecta?); variable nail dystrophy; variable palmoplantar keratoderma, hyperkeratosis, reduced sweating
Penetrance for gene: NECTIN4 were set to Complete
Review for gene: NECTIN4 was set to GREEN
Added comment: Evidence from literature is that loss of function variants in NECTIN4 lead to a syndromic phenotype which includes "enamel hypoplasia" a term often used when amelogenesis imperfecta occurs with other symptoms.

PMID:34067522 describes ectodermal dysplasia-syndactyly syndrome 1 (EDSS1) characterized by cutaneous syndactyly of the toes and fingers and abnormalities of the hair and teeth, variably associated with nail dystrophy and palmoplantar keratoderma (PPK). EDSS1 is caused by biallelic mutations in the NECTIN4. Nine other EDSS1 cases have been described prior to this report. 5.5-year-old female child affected with EDSS1 due to the novel homozygous frameshift mutation c.1150delC (p.Gln384ArgfsTer7) in NECTIN4. The patient presents brittle scalp hair, sparse eyebrows and eyelashes, widely spaced conical teeth and dental agenesis, as well as toenail dystrophy and mild PPK. She has minimal proximal syndactyly limited to toes 2–3, which makes the phenotype of our patient peculiar as the overt involvement of both fingers and toes is typical of EDSS1. All previously described mutations are located in the nectin-4 extracellular portion, whereas p.Gln384ArgfsTer7 occurs within the cytoplasmic domain of the protein. This mutation is predicted to affect the interaction with afadin, suggesting that impaired afadin activation is sufficient to determine EDSS1.

PMID 37183149 reported a large Pakistani consanguineous family, the affected individuals presented the classical EDSS1 clinical features including sparse hair, hypoplastic nails with thick flat discolored nail plates, peg-shaped, conical, and widely spaced teeth with enamel hypoplasia, proximal cutaneous syndactyly of fingers and toes. NECTIN4 novel nonsense variant [c.163C>T; p.(Arg55*)]. Most likely Nectin-4 function will be lost.
Sources: Literature
Amelogenesis imperfecta v4.5 AIRE Claire Smith changed review comment from: It is well reported that 70-90% of patients with APS-1 (# 240300) have enamel formation defects of various severity. These patients have mutations in the AIRE gene (see PMID 19393987;27253668).

Paper in 2023 (PMID 37993717) reported that there is autoreactivity against enamel antigens in Aire-/- mouse models and that this is also seen in (against ameloblast-specific proteins) in patients with APS-1. The authors looked at 17 patients total and saw autoantibodies in all to enamel specific proteins, see figure 1F.

Immunofluorescence microscopy analysis demonstrated largely overlapping signals from APS-1 serum with that from AMELX- and LAMB3-specific antibodies. Moreover, ELISA analyses revealed that both paediatric and adult patients with APS-1 have IgA autoantibodies against several ameloblast antigens, including LAMB3, FAM20A, ENAM and AMELX, or IgG1 autoantibodies against ACPT. Overall, all patients tested with APS-1 developed autoantibodies against at least one of the five major ameloblast antigens, with distinct reactivity clusters. Furthermore, patients with severe enamel defects had significantly higher levels of autoantibody reactivity against all of the tested enamel antigens compared with those with mild enamel defects or age-matched healthy control individuals. Moreover, canines, which have the longest mineralization period (around 6.5 years), had the most pronounced enamel defects, in comparison to incisors or first molars, of which the mineralization period is significantly shorter (around 4.5 and 3  years, respectively), suggesting that the longer the mineralization period, the higher the chance for enamel-specific autoantibodies to interfere and cause damage in enamel formation.

This is a really interesting mechanism of disease, whereby mutations in AIRE can cause the development of self antigens against the proteins that make enamel, which leads to amelogenesis imperfecta. Note that the paper does not specify whether patients were mono or biallelic carriers of the AIRE variants, note that OMIM records that both mono and balletic variants can cause APS-1.

Note that the authors also looked at patients with coeliac disease and found similar autoantibodies against enamel proteins.
Sources: Literature; to: It is well reported that 70-90% of patients with APS-1 (# 240300) have enamel formation defects of various severity. These patients have mutations in the AIRE gene (see PMID 19393987;27253668).

Paper in 2023 (PMID 37993717) reported that there is autoreactivity against enamel antigens in Aire-/- mouse models and that this is also seen in (against ameloblast-specific proteins) in patients with APS-1. The authors looked at 17 patients total and saw autoantibodies in all to enamel specific proteins, see figure 1F.

Immunofluorescence microscopy analysis demonstrated largely overlapping signals from APS-1 serum with that from AMELX- and LAMB3-specific antibodies. Moreover, ELISA analyses revealed that both paediatric and adult patients with APS-1 have IgA autoantibodies against several ameloblast antigens, including LAMB3, FAM20A, ENAM and AMELX, or IgG1 autoantibodies against ACPT. Overall, all patients tested with APS-1 developed autoantibodies against at least one of the five major ameloblast antigens, with distinct reactivity clusters. Furthermore, patients with severe enamel defects had significantly higher levels of autoantibody reactivity against all of the tested enamel antigens compared with those with mild enamel defects or age-matched healthy control individuals. Moreover, canines, which have the longest mineralization period (around 6.5 years), had the most pronounced enamel defects, in comparison to incisors or first molars, of which the mineralization period is significantly shorter (around 4.5 and 3  years, respectively), suggesting that the longer the mineralization period, the higher the chance for enamel-specific autoantibodies to interfere and cause damage in enamel formation.

This is a really interesting mechanism of disease, whereby mutations in AIRE can cause the development of self antigens against the proteins that make enamel, which leads to amelogenesis imperfecta. Note that the paper does not specify whether patients were mono or biallelic carriers of the AIRE variants, note that OMIM records that both mono and balletic variants can cause APS-1.

Note that the authors also looked at patients with coeliac disease and found similar autoantibodies against enamel proteins.
Sources: Literature

Edit: I didn't add Amelogenesis imperfecta to the phenotype list. Can you please add this! I can't seem to add it in retrospect!
Amelogenesis imperfecta v4.5 AIRE Claire Smith gene: AIRE was added
gene: AIRE was added to Amelogenesis imperfecta. Sources: Literature
Mode of inheritance for gene: AIRE was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Publications for gene: AIRE were set to PMID: 37993717; 19393987; 27253668
Phenotypes for gene: AIRE were set to Addison disease; hypoparathyroidism; chronic mucocutaneous candidiasis
Penetrance for gene: AIRE were set to unknown
Review for gene: AIRE was set to GREEN
Added comment: It is well reported that 70-90% of patients with APS-1 (# 240300) have enamel formation defects of various severity. These patients have mutations in the AIRE gene (see PMID 19393987;27253668).

Paper in 2023 (PMID 37993717) reported that there is autoreactivity against enamel antigens in Aire-/- mouse models and that this is also seen in (against ameloblast-specific proteins) in patients with APS-1. The authors looked at 17 patients total and saw autoantibodies in all to enamel specific proteins, see figure 1F.

Immunofluorescence microscopy analysis demonstrated largely overlapping signals from APS-1 serum with that from AMELX- and LAMB3-specific antibodies. Moreover, ELISA analyses revealed that both paediatric and adult patients with APS-1 have IgA autoantibodies against several ameloblast antigens, including LAMB3, FAM20A, ENAM and AMELX, or IgG1 autoantibodies against ACPT. Overall, all patients tested with APS-1 developed autoantibodies against at least one of the five major ameloblast antigens, with distinct reactivity clusters. Furthermore, patients with severe enamel defects had significantly higher levels of autoantibody reactivity against all of the tested enamel antigens compared with those with mild enamel defects or age-matched healthy control individuals. Moreover, canines, which have the longest mineralization period (around 6.5 years), had the most pronounced enamel defects, in comparison to incisors or first molars, of which the mineralization period is significantly shorter (around 4.5 and 3  years, respectively), suggesting that the longer the mineralization period, the higher the chance for enamel-specific autoantibodies to interfere and cause damage in enamel formation.

This is a really interesting mechanism of disease, whereby mutations in AIRE can cause the development of self antigens against the proteins that make enamel, which leads to amelogenesis imperfecta. Note that the paper does not specify whether patients were mono or biallelic carriers of the AIRE variants, note that OMIM records that both mono and balletic variants can cause APS-1.

Note that the authors also looked at patients with coeliac disease and found similar autoantibodies against enamel proteins.
Sources: Literature
Amelogenesis imperfecta v4.1 LAMC2 Claire Smith edited their review of gene: LAMC2: Added comment: PMID: 37228816 Bloch-Zupan et al. 2023 report one family with LAMC2 mutations as part of a larger panel of sequenced individuals. They report a single child as being affected with a hypoplastic/hypomature AI phenotype. The primary dentition is described as showing thin white opaque enamel.

They identified a heterozygous LAMC2 variant NM_005562.3: c.493C>T; p.(Arg165Cys) with an allele frequency of 0.2% in GnomAD, predicted deleterious by SIFT (v4.0.3) and PolyPhen-2 and located in the Laminin EGF domain. The authors highlight that the enamel formation defects in mice (Wazen et al., 2016) and the patient’s phenotype are similar to the one another. The allele is inherited from her mother but the mother's phenotype was not available.

Notably the patient was sequenced using whole exome sequencing using the following parameters: Non-pathogenic variants were filtered out via: 1) variants represented with an allele frequency of more than 1% in public variation databases including the 1,000 Genomes, the GnomAD database or their internal exome database, variants in 5′ or 3′ UTR, variants with intronic locations and no prediction of local splice effect, and synonymous variants without pathogenic prediction of local splice effect.

Annotations of structural variations (SV) were performed by AnnotSV (Geoffroy et al., 2018). No other findings are presented for the individual.

In conclusion, I do not believe this is strong enough evidence to conclude that this LAMC2 mutation is the cause of disease in this family due to the lack of phenotype information for the mother or any modelling of the effects of the variant, but it is suggestive and additional publications with further families might provide more solid evidence to elevate this gene to green. I would currently consider this gene to be rated amber.; Changed rating: AMBER; Changed mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Amelogenesis imperfecta v2.20 COL17A1 Arina Puzriakova Phenotypes for gene: COL17A1 were changed from Epidermolysis bullosa, junctional, non-Herlitz type, 226650 (includes enamel pitting); Amelogenesis Imperfecta; non-Herlitz junctional epidermolysis bullosa (nH-JEB) and amelogenesis imperfecta; hypoplastic amelogenesis imperfecta to Epidermolysis bullosa, junctional 4, intermediate, OMIM:619787 (includes enamel pitting); Hypoplastic amelogenesis imperfecta
Amelogenesis imperfecta v2.13 PEX26 Eleanor Williams Phenotypes for gene: PEX26 were changed from Peroxisome biogenesis disorder 7A (Zellweger), 614872; Peroxisome biogenesis disorder 7B, 614873; Heimler syndrome; Amelogenesis imperfecta; enamel dysplasia to Amelogenesis Imperfecta, MONDO:0019507; Heimler syndrome
Amelogenesis imperfecta v1.14 DLX3 Eleanor Williams Phenotypes for gene: DLX3 were changed from Amelogenesis imperfecta, type IV, 104510; Amelogenesis Imperfecta, Type IV, 104510; Amelogenesis Imperfecta, Dominant; amelogenesis imperfecta with taurodontism; Trichodontoosseous syndrome, 190320; Tricho-dento-osseous syndrome (TDO) (includes enamel hypoplasia); hypoplastic AI, taurodontism and kinky hair to Amelogenesis imperfecta, type IV, 104510; Amelogenesis Imperfecta, Type IV, 104510; Amelogenesis Imperfecta, Dominant; amelogenesis imperfecta with taurodontism; Trichodontoosseous syndrome, 190320; Tricho-dento-osseous syndrome (TDO) (includes enamel hypoplasia); hypoplastic AI, taurodontism and kinky hair; Tricho-Dento-Osseous syndrome , Amelogenesis Imperfecta, hypoplastic
Amelogenesis imperfecta v1.7 RELT Claire Smith gene: RELT was added
gene: RELT was added to Amelogenesis imperfecta. Sources: Literature
Mode of inheritance for gene: RELT was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: RELT were set to PMID: 30506946
Phenotypes for gene: RELT were set to amelogenesis imperfecta (hypoplastic)
Penetrance for gene: RELT were set to Complete
Review for gene: RELT was set to GREEN
Added comment: PMID: 30506946 present evidence of three consanguineous Turkish families with irregular hypoplastic amelogenesis imperfecta. The authors also present a Relt-/- mouse model with incisor and molar enamel malformations. RELT should be included as a causative gene in diagnostic panels for AR AI in future.
Sources: Literature
Amelogenesis imperfecta ENAM Rebecca Foulger marked ENAM as ready
Amelogenesis imperfecta ENAM Rebecca Foulger classified ENAM as green
Amelogenesis imperfecta ENAM Claire Smith reviewed ENAM
Amelogenesis imperfecta ENAM Rebecca Foulger commented on ENAM