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Intellectual disability

Gene: ANTXR1

Red List (low evidence)
ANTXR1 (anthrax toxin receptor 1)
EnsemblGeneIds (GRCh38): ENSG00000169604
EnsemblGeneIds (GRCh37): ENSG00000169604
OMIM: 606410, Gene2Phenotype
ANTXR1 is in 9 panels

3 reviews

Ida Ertmanska (Genomics England Curator)

Red List (low evidence)

Comment on list classification: While there are over a 100 individuals reported with GAPO syndrome and biallelic ANTXR1 variants, intellectual disability is not a feature of this syndrome. Hence, this gene should be rated Red on Intellectual disability.
Created: 23 Oct 2026, 10:03 a.m. | Last Modified: 23 Oct 2026, 10:03 a.m.
Panel Version: 11.45
PMID: 40962491 Modafferi et al., 2025
Review of 105 GAPO syndrome cases + new case: report of a 33yo woman with GAPO syndrome a homozygous ANTXR1 deletion of exons 4, 5, and 6. The newly reported individual had short stature (130cm), craniofacial abnormalities, absence of several dental elements, liver disease/hepatomegaly, blindness secondary to optic atrophy, alopecia, primary amenorrhea, and progeroid appearance of the skin.
Literature review describes a common phenotype: growth impairment, alopecia, sparse dentition (97/105), long bone dysplasia, optic atrophy (48/105) & other ocular features. Intellectual disability is not a common feature of the syndrome - cognitive function was explicitly reported to be normal in 27 cases, and not mentioned in others.
Both missense, splice, and frameshift variants in ANTXR1 have been reported to cause GAPO syndrome.

PMID: 38423276 Balakrishnan, Goud, & Teegala, 2024
Report of an Indian proband, 3.75yrs old female, with GAPO syndrome. She presented with short stature, reduced length of long bones, dysmorphism, sparse hair growth & lack of appropriate dentition. She was born with sagittal craniosynostosis and right club foot. Patient was noted to have mild dev delay with preserved intellect and social skills. Her head circumference was 49.5 cms (-1.1 Z score), height was 82 cms (−4.5 Z score). Trio exome detected a homozygous ANTXR1 NM_032208.3: c.568delC (p. Arg190GlyfsTer12) variant in the proband - het in parents.

PMID: 30575274 Abdel-Hamid et al., 2019
Report of 7 patients from 5 unrelated consanguineous Egyptian families with GAPO syndrome and ANTXR1 variants. Common phenotype: alopecia, pseudoadontia, micrognathia, dysmorphism (e.g., frontal bossing, hypertelorism) optic atrophy (6/7), glaucoma (unilateral or bilateral), short stature, microcephaly (7/7, including 3 unrelated patients with severe microcephaly of more than -3 SD), joint hyperextensibility. Craniosynostosis and keratopathy noted in only 1/7 individuals. Intellectual disability not reported.
Individuals harboured 5 different homozygous ANTXR1 variants: 2 splice variants, 2 frameshift variants, and 1 deletion. Their parents were heterozygous and unaffected.

ANTXR1 association with AR GAPO syndrome is classified as Definitive in ClinGen (Syndromic Disorders GCEP, July 2025).
Created: 22 Oct 2026, 2:54 p.m. | Last Modified: 23 Oct 2026, 10:11 a.m.
Panel Version: 11.48

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
GAPO syndrome, OMIM:230740; GAPO syndrome, MONDO:0009263; Growth delay-alopecia-pseudoanodontia-optic atrophy syndrome

Publications

Created: 22 Oct 2026, 2:54 p.m.
Last Modified: 23 Oct 2026, 10:11 a.m.
Panel version: 11.45

BRIDGE consortium (NIHRBR-RD)

Green List (high evidence)

This is a pertinent gene from the NIHR BioResource - Rare Diseases Study (NIHRBR-RD) BRIDGE Study : SPEED (Specialist Pathology: Evaluating Exomes in Diagnostics) which covers epilepsies, movement and microcephaly disorders, this gene is on the SPEED_NEURO_20170705 gene list. Evidences used for SPEED NEURO gene list: in_ddg2p_20141118_conf;in_ddg2p_20141118_conf;in_ddg2p_201507;in_ddg2p_201507_conf;in_ddg2p_2_4_2017;in_ddg2p_2_4_2017_conf;in_gilissen_2014_known . Main mutation mechanism : Loss of function
Created: 27 Jul 2017, 5:04 p.m.
Evidences key, gene present in following gene lists and main mutation mechanism : ddg2p_20141118; ddg2p_20141118_conf; ddg2p_201507; ddg2p_201507_conf; gilissen_2014_known; Nijmegen_ID_diagnostic; neuro_20160418_strict; Loss of function. This is a pertinent gene from the BRIDGE Study : SPEED (Specialist Pathology: Evaluating Exomes in Diagnostics) which covers epilepsies, movement and microcephaly disorders, this gene comes from the SPEED_NEURO_v3.0_20170404 gene list. The following experts from the BRIDGE consortium NIHRBR-RD contributed to this panel: - Professor F. Lucy Raymond, Cambridge Institute for Medical Research, University of Cambridge - Manju Kurian, Paediatric neurologist, Great Ormond Street Hosptial - Keren Carss, NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust - Alba Sanchis-Juan, NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust - Marie Erwood NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust - Louise Daugherty, NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust
Created: 19 Jul 2017, 11:59 a.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Publications

Created: 2 Aug 2017, 2:23 p.m.

Panel version: 1.354

Louise Daugherty (Genomics England Curator)

Comment on list classification: This gene is from an expert list and needs further assessment by the Genomics England curation team to access inclusion and pertinence to this panel.
Created: 19 Jul 2017, 4:48 p.m.
Created: 19 Jul 2017, 4:48 p.m.

Panel version: 1.170

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Red
Phenotypes
  • GAPO syndrome, OMIM:230740
  • GAPO syndrome, MONDO:0009263
  • Growth delay-alopecia-pseudoanodontia-optic atrophy syndrome
OMIM
606410
Clinvar variants
Variants in ANTXR1
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

23 Oct 2026, Gel status: 1

Set Phenotypes

Ida Ertmanska (Genomics England Curator)

Phenotypes for gene: ANTXR1 were changed from {Hemangioma, capillary infantile, susceptibility to}, 602089; GAPO syndrome, 230740 to GAPO syndrome, OMIM:230740; GAPO syndrome, MONDO:0009263; Growth delay-alopecia-pseudoanodontia-optic atrophy syndrome

23 Oct 2026, Gel status: 1

Set publications

Ida Ertmanska (Genomics England Curator)

Publications for gene: ANTXR1 were set to

23 Oct 2026, Gel status: 1

Entity classified by Genomics England curator

Ida Ertmanska (Genomics England Curator)

Gene: antxr1 has been classified as Red List (Low Evidence).

12 Mar 2018, Gel status: 2

Panel promoted to version 2.0

Ellen McDonagh (Genomics England Curator)

12.03.2018: Due to major updates completed (Phase 1, 2 and 3), this panel was promoted to Version 2 in order to reflect the major updates since November 2017 which have resulted in reviews for 836 genes added by Genomics England Curators and the Clinical Team, 130 new Green genes added to the interpretation pipeline (from 751 to 881 Green genes), and the gene total has increased from 1879 to 1927.

19 Jul 2017, Gel status: 2

Gene classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

This gene has been classified as Amber List (Moderate Evidence).

19 Jul 2017, Gel status: 0

Created

BRIDGE consortium (NIHRBR-RD)

ANTXR1 was created by BRIDGE

19 Jul 2017, Gel status: 0

Added New Source

BRIDGE consortium (NIHRBR-RD)

ANTXR1 was added to Intellectual disabilitypanel. Sources: BRIDGE study SPEED NEURO Tier1 Gene