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Intellectual disability

Gene: PDCD6IP

Amber List (moderate evidence)
PDCD6IP (programmed cell death 6 interacting protein)
EnsemblGeneIds (GRCh38): ENSG00000170248
EnsemblGeneIds (GRCh37): ENSG00000170248
OMIM: 608074, Gene2Phenotype
PDCD6IP is in 3 panels

3 reviews

Ida Ertmanska (Genomics England Curator)

I don't know

PMID: 40897677 D'Alessio et al., 2025
Report of a male individual with mild intellectual disability and acquired microcephaly carrying a homozygous nonsense variant in PDCD6IP: NM_013374.6 c.964C>T p.(Arg322*). Heterozygous family members unaffected. Additional features of strabismus and thrombocytopenia was also noted. No seizures present. Proband OFC listed as 52.7cm (−2.5 SD) in table 1. At birth, his OFC was 34 cm (−0.78 SD), but at age 25 yrs, his OFC was 51.6 cm (−3.1 SD).
Created: 13 Aug 2026, 4:33 p.m. | Last Modified: 13 Aug 2026, 4:33 p.m.
Panel Version: 11.7

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
?Microcephaly 29, primary, autosomal recessive, OMIM:620047; microcephaly 29, primary, autosomal recessive, MONDO:0031060

Publications

Created: 13 Aug 2026, 4:33 p.m.
Last Modified: 13 Aug 2026, 4:33 p.m.
Panel version: 11.7

Arina Puzriakova (Genomics England Curator)

Comment on list classification: Phenotype is relevant to this panel with a supportive animal model that recapitulates features such as microcephaly. However, additional cases required to validate pathogenicity prior to inclusion as diagnostic-grade. Therefore Rating Amber, awaiting further publications.
Created: 27 Aug 2020, 12:15 p.m. | Last Modified: 4 Jun 2021, 12:20 p.m.
Panel Version: 3.1110
Created: 27 Aug 2020, 12:15 p.m.
Last Modified: 4 Jun 2021, 12:20 p.m.
Panel version: 3.269

Zornitza Stark (Australian Genomics)

I don't know

One consanguineous family with 2 affected sibs with primary microcephaly (-4SD), intellectual disability and short stature (-5/6SD), and homozygous frameshift variant in PDCD6IP. The homozygous variant was confirmed in both affected sibs, while the four healthy siblings and parents were heterozygous. The clinical features observed in the patients were similar to the phenotypes observed in mouse and zebrafish models of PDCD6IP mutations in previous studies.
Sources: Literature
Created: 1 Jul 2020, 9:46 a.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
microcephaly; Intellectual disability

Publications

Created: 1 Jul 2020, 9:46 a.m.

Panel version: 3.126

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Amber
Phenotypes
  • ?Microcephaly 29, primary, autosomal recessive, OMIM:620047
  • microcephaly 29, primary, autosomal recessive, MONDO:0031060
OMIM
608074
Clinvar variants
Variants in PDCD6IP
Penetrance
None
Publications
Panels with this gene

History Filter Activity

14 Aug 2026, Gel status: 2

Set Phenotypes

Achchuthan Shanmugasundram (Genomics England Curator)

Phenotypes for gene: PDCD6IP were changed from microcephaly; Intellectual disability to ?Microcephaly 29, primary, autosomal recessive, OMIM:620047; microcephaly 29, primary, autosomal recessive, MONDO:0031060

14 Aug 2026, Gel status: 2

Set publications

Achchuthan Shanmugasundram (Genomics England Curator)

Publications for gene: PDCD6IP were set to 32286682

27 Aug 2020, Gel status: 2

Entity classified by Genomics England curator

Arina Puzriakova (Genomics England Curator)

Gene: pdcd6ip has been classified as Amber List (Moderate Evidence).

1 Jul 2020, Gel status: 0

Created, Added New Source, Set mode of inheritance, Set publications, Set Phenotypes

Zornitza Stark (Australian Genomics)

gene: PDCD6IP was added gene: PDCD6IP was added to Intellectual disability. Sources: Literature Mode of inheritance for gene: PDCD6IP was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: PDCD6IP were set to 32286682 Phenotypes for gene: PDCD6IP were set to microcephaly; Intellectual disability Review for gene: PDCD6IP was set to AMBER