HLA-C

major histocompatibility complex, class I, C, the group of C1-set domain containing|Histocompatibility complex

Basic information

Region (hg38): 6:31268749-31272130

Previous symbols: [ "HLA-JY3", "D6S204", "PSORS1" ]

Links

ENSG00000204525 ∙ NCBI:3107 ∙ OMIM:142840 ∙ HGNC:4933 ∙ Uniprot:P10321 ∙ 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 HLA-C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HLA-C 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				1		1
missense				1	1	2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	2	1

Variants in HLA-C

This is a list of pathogenic ClinVar variants found in the HLA-C region.

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

Position	Type	Phenotype	Significance	ClinVar
6-31269491-A-C			not provided (-)
6-31269526-C-A			not provided (-)
6-31271845-C-A			Benign (Feb 18, 2020)
6-31271872-G-A		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
6-31272002-C-T			Likely benign (Mar 01, 2024)
6-31272048-G-A			Likely benign (Jul 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HLA-C	protein_coding	protein_coding	ENST00000376228	8	3382

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000157	0.864	121260	91	4381	125732	0.0179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.135	193	198	0.973	0.00000976	2164
Missense in Polyphen		83	105.58	0.78614		1247
Synonymous	0.157	83	84.8	0.978	0.00000444	699
Loss of Function	1.51	12	19.1	0.628	8.29e-7	202

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0224	0.0189
Ashkenazi Jewish	0.0110	0.00787
East Asian	0.00913	0.00846
Finnish	0.0315	0.0253
European (Non-Finnish)	0.0309	0.0236
Middle Eastern	0.00913	0.00846
South Asian	0.0214	0.0178
Other	0.0199	0.0156

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the presentation of foreign antigens to the immune system.
• Pathway: Antigen processing and presentation - Homo sapiens (human);Cell adhesion molecules (CAMs) - Homo sapiens (human);Type I diabetes mellitus - Homo sapiens (human);Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human);Allograft rejection - Homo sapiens (human);Graft-versus-host disease - Homo sapiens (human);Viral myocarditis - Homo sapiens (human);Endocytosis - Homo sapiens (human);Autoimmune thyroid disease - Homo sapiens (human);Phagosome - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Natural killer cell mediated cytotoxicity - Homo sapiens (human);Viral carcinogenesis - Homo sapiens (human);Cellular senescence - Homo sapiens (human);Epstein-Barr virus infection - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Herpes simplex infection - Homo sapiens (human);Proteasome Degradation;Allograft Rejection;Neutrophil degranulation;DAP12 interactions;Cytokine Signaling in Immune system;Innate Immune System;Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System;Endosomal/Vacuolar pathway;Antigen processing-Cross presentation;Class I MHC mediated antigen processing & presentation;Interferon gamma signaling;Interferon alpha/beta signaling;Antigen Presentation: Folding, assembly and peptide loading of class I MHC;Interferon Signaling (Consensus)

Recessive Scores

• pRec: 0.799

Intolerance Scores

• loftool: 0.954
• rvis_EVS: 7.65
• rvis_percentile_EVS: 99.92

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.401

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.633

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Gene ontology

• Biological process: positive regulation of T cell mediated cytotoxicity;antigen processing and presentation of peptide antigen via MHC class I;antigen processing and presentation of endogenous peptide antigen via MHC class Ib;antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent;antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent;antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent;immune response;regulation of immune response;interferon-gamma-mediated signaling pathway;type I interferon signaling pathway
• Cellular component: Golgi membrane;extracellular space;endoplasmic reticulum;Golgi apparatus;plasma membrane;external side of plasma membrane;cell surface;ER to Golgi transport vesicle membrane;phagocytic vesicle membrane;early endosome membrane;MHC class I protein complex;recycling endosome membrane;integral component of lumenal side of endoplasmic reticulum membrane
• Molecular function: signaling receptor binding;protein binding;peptide antigen binding