PCYT1B

phosphate cytidylyltransferase 1B, choline

Basic information

Region (hg38): X:24558086-24672677

Links

ENSG00000102230 ∙ NCBI:9468 ∙ OMIM:300948 ∙ HGNC:8755 ∙ Uniprot:Q9Y5K3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PCYT1B gene.

• Inborn genetic diseases (4 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCYT1B gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2		2
missense			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	4	2	0

Variants in PCYT1B

This is a list of pathogenic ClinVar variants found in the PCYT1B region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
X-24562362-G-A			Likely benign (Feb 01, 2023)
X-24562409-G-A		not specified	Uncertain significance (Jan 09, 2024)
X-24562475-T-G		not specified	Uncertain significance (Apr 04, 2023)
X-24575238-A-G			Likely benign (Feb 01, 2023)
X-24590024-T-C		not specified	Uncertain significance (May 27, 2022)
X-24590181-C-T			Likely benign (Nov 01, 2023)
X-24619030-G-T		not specified	Uncertain significance (Nov 15, 2021)
X-24619040-C-G		not specified	Uncertain significance (Jan 17, 2024)
X-24647045-C-T		not specified	Uncertain significance (Jul 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCYT1B	protein_coding	protein_coding	ENST00000379144	8	114591

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.897	0.103	125701	1	1	125703	0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.16	65	136	0.479	0.0000107	2424
Missense in Polyphen		11	39.73	0.27687		667
Synonymous	-0.499	56	51.5	1.09	0.00000424	691
Loss of Function	2.91	1	11.8	0.0850	8.18e-7	227

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000256	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Controls phosphatidylcholine synthesis.
• Pathway: Glycerophospholipid metabolism - Homo sapiens (human);Choline metabolism in cancer - Homo sapiens (human);Phosphonate and phosphinate metabolism - Homo sapiens (human);Kennedy pathway from Sphingolipids;One carbon metabolism and related pathways;Metabolism of lipids;phosphatidylcholine biosynthesis;Metabolism;Synthesis of PC;Glycerophospholipid metabolism;Glycerophospholipid biosynthesis;Phospholipid metabolism (Consensus)

Recessive Scores

• pRec: 0.134

Intolerance Scores

• loftool: 0.0434
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.76

Haploinsufficiency Scores

• pHI: 0.194
• hipred: Y
• hipred_score: 0.728
• ghis: 0.690

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.984

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Pcyt1b
• Phenotype: neoplasm; reproductive system phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: ovarian follicle development;phosphatidylcholine biosynthetic process;CDP-choline pathway;spermatogenesis
• Cellular component: cytoplasm;endoplasmic reticulum membrane
• Molecular function: choline-phosphate cytidylyltransferase activity;phosphatidylcholine binding