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Intellectual disability

Gene: PCYT1A

Red List (low evidence)

PCYT1A (phosphate cytidylyltransferase 1, choline, alpha)
EnsemblGeneIds (GRCh38): ENSG00000161217
EnsemblGeneIds (GRCh37): ENSG00000161217
OMIM: 123695, Gene2Phenotype
PCYT1A is in 8 panels

3 reviews

Helen Brittain (Genomics England Curator)

Red List (low evidence)

No clear evidence for ID. Is already on the posterior segment and unexplained skeletal panels.
Created: 28 Nov 2017, 3:55 p.m.

BIALLELIC, autosomal or pseudoautosomal

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 . Main mutation mechanism : Loss of function
Created: 27 Jul 2017, 7:57 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal


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: 28 Jul 2017, 3:10 p.m.


Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
  • Expert Review Red
  • Spondylometaphyseal dysplasia with cone-rod dystrophy, 608940
Clinvar variants
Variants in PCYT1A
Panels with this gene

History Filter Activity

11 Feb 2021, Gel status: 1

Clear Sources

Sarah Leigh (Genomics England Curator)

Source: Expert Review Amber was removed from gene: PCYT1A

12 Mar 2018, Gel status: 1

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.

29 Nov 2017, Gel status: 1

Added New Source

Ellen McDonagh (Genomics England Curator)

Expert Review Red was added to PCYT1A. Panel: Intellectual disability

28 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).

27 Jul 2017, Gel status: 0

Added New Source

BRIDGE consortium (NIHRBR-RD)

PCYT1A was added to Intellectual disabilitypanel. Sources: BRIDGE study SPEED NEURO Tier1 Gene

27 Jul 2017, Gel status: 0


BRIDGE consortium (NIHRBR-RD)

PCYT1A was created by BRIDGE