Intellectual disability
Gene: PHF5A

PHF5A (PHD finger protein 5A)
EnsemblGeneIds (GRCh38): ENSG00000100410
EnsemblGeneIds (GRCh37): ENSG00000100410
PHF5A is in 3 panels

1 review

Arina Puzriakova (Genomics England Curator)

Green List (high evidence)

Comment on list classification: At least 10 unrelated individuals have been reported with de novo variants in the PHF5A gene. Syndromic developmental delay is reported in at least 9 of those cases, with five individuals developing intellectual disability later in life. Inclusion on this panel would also enable inclusion of the R27 Paediatric disorders super panel which appears relevant to the presentation. Therefore, this gene should be promoted to Green at the next GMS panel update.
Created: 5 Mar 2026, 2:13 p.m. | Last Modified: 5 Mar 2026, 2:13 p.m.

Panel Version: 9.287

PMID: 33811463 - de novo nonsense variant c.162C>A / p.(Tyr54*) in PHF5A was reported in a patient with left microtia and bilateral absence of 12th ribs

PMID: 37422718 - 9 unrelated individuals with congenital malformations, including preauricular tags and hypospadias, short stature, subtle skeletal features, craniofacial dysmorphism. All had developmental delay, and five individuals developed ID later in life (1 severe, 4 mild). All harboured de novo heterozygous PHF5A variants, including 4 nonsense, 3 missense, 1 splice, and 1 start-loss variant.
Sources: Literature
Created: 5 Mar 2026, 11:48 a.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
PHF5A-related neurodevelopmental disorder with congenital malformations

Publications

Created: 5 Mar 2026, 11:48 a.m.

Panel version: 9.286

Details

Mode of Inheritance

MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Sources

Expert Review Amber
Literature

Phenotypes

PHF5A-related neurodevelopmental disorder with congenital malformations

Tags

Q1_26_promote_green

Clinvar variants

Variants in PHF5A

Penetrance

None

Publications

Panels with this gene

History Filter Activity

5 Mar 2026, Gel status: 2

Entity classified by Genomics England curator

Arina Puzriakova (Genomics England Curator)

Gene: phf5a has been classified as Amber List (Moderate Evidence).

5 Mar 2026, Gel status: 1

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

Arina Puzriakova (Genomics England Curator)

gene: PHF5A was added gene: PHF5A was added to Intellectual disability. Sources: Literature Q1_26_promote_green tags were added to gene: PHF5A. Mode of inheritance for gene: PHF5A was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: PHF5A were set to 33811463; 37422718 Phenotypes for gene: PHF5A were set to PHF5A-related neurodevelopmental disorder with congenital malformations Review for gene: PHF5A was set to GREEN

Intellectual disability Gene: PHF5A