PCYT2

phosphate cytidylyltransferase 2, ethanolamine

Basic information

Region (hg38): 17:81900958-81911432

Links

ENSG00000185813 ∙ NCBI:5833 ∙ OMIM:602679 ∙ HGNC:8756 ∙ Uniprot:Q99447 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spastic paraplegia 82, autosomal recessive (Moderate), mode of inheritance: AR
• spastic paraplegia 82, autosomal recessive (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spastic paraplegia 82, autosomal recessive	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic; Ophthalmologic	31637422

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PCYT2 gene.

• Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCYT2 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				7	1	8
missense		2	40	2		44
nonsense		2				2
start loss						0
frameshift	1		1			2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region		1	3	1	3	8
non coding			16	1	5	22
Total	1	4	57	10	6

Highest pathogenic variant AF is 0.00000657

Variants in PCYT2

This is a list of pathogenic ClinVar variants found in the PCYT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-81902300-C-T		not specified	Likely benign (Feb 26, 2025)
17-81902312-T-C		not specified	Uncertain significance (Aug 04, 2023)
17-81902335-C-T		not specified	Uncertain significance (Oct 06, 2022)
17-81902368-G-A		not specified	Uncertain significance (May 13, 2024)
17-81902378-C-T		not specified	Uncertain significance (Oct 17, 2024)
17-81902399-C-G		not specified	Uncertain significance (Dec 13, 2023)
17-81902411-C-G		not specified	Uncertain significance (Aug 22, 2022)
17-81902414-G-A		not specified	Uncertain significance (May 10, 2024)
17-81902420-G-A		not specified	Uncertain significance (Sep 22, 2021)
17-81902426-C-T		not specified	Uncertain significance (Dec 15, 2022)
17-81902462-C-T			Likely benign (Aug 01, 2024)
17-81902495-A-G		not specified	Uncertain significance (Dec 25, 2024)
17-81902513-G-A			Likely benign (Mar 01, 2025)
17-81902515-C-A		not specified	Uncertain significance (Sep 16, 2021)
17-81902524-C-G		not specified	Uncertain significance (Dec 17, 2023)
17-81902629-G-T		not specified	Uncertain significance (Jan 24, 2025)
17-81902676-C-A		not specified	Uncertain significance (Feb 15, 2023)
17-81902687-C-T		not specified	Uncertain significance (Jul 30, 2024)
17-81902717-C-T		not specified	Uncertain significance (Jul 25, 2024)
17-81902740-G-A		not specified	Uncertain significance (Aug 12, 2021)
17-81902744-C-G		not specified	Uncertain significance (Jul 30, 2024)
17-81904728-C-G			Benign (May 24, 2021)
17-81904754-G-A			Benign (May 15, 2021)
17-81904847-C-T		Inborn genetic diseases	Uncertain significance (Mar 06, 2023)
17-81904856-C-A		Inborn genetic diseases	Uncertain significance (Jan 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCYT2	protein_coding	protein_coding	ENST00000538721	14	10500

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000864	0.996	125691	0	20	125711	0.0000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.73	169	245	0.689	0.0000153	2651
Missense in Polyphen		44	87.114	0.50509		798
Synonymous	-0.735	108	98.7	1.09	0.00000658	779
Loss of Function	2.62	9	22.4	0.402	0.00000105	268

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000273	0.000272
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000116	0.000114
Middle Eastern	0.00	0.00
South Asian	0.0000331	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays an important role in the biosynthesis of the phospholipid phosphatidylethanolamine. Catalyzes the formation of CDP-ethanolamine.
• Pathway: Glycerophospholipid metabolism - Homo sapiens (human);Phosphonate and phosphinate metabolism - Homo sapiens (human);Lamivudine Pathway, Pharmacokinetics/Pharmacodynamics;Lamivudine Metabolism Pathway;Kennedy pathway from Sphingolipids;One carbon metabolism and related pathways;Metabolism of lipids;Metabolism;Synthesis of PE;phosphatidylethanolamine biosynthesis II;Glycerophospholipid biosynthesis;Phospholipid metabolism (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.133
• rvis_EVS: -0.45
• rvis_percentile_EVS: 24.19

Haploinsufficiency Scores

• pHI: 0.315
• hipred: Y
• hipred_score: 0.735
• ghis: 0.585

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.858

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcyt2
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); liver/biliary system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: phosphatidylethanolamine biosynthetic process;phospholipid biosynthetic process
• Cellular component: cellular_component;endoplasmic reticulum membrane
• Molecular function: ethanolamine-phosphate cytidylyltransferase activity