HM13

histocompatibility minor 13, the group of Peptidase family A22

Basic information

Region (hg38): 20:31514428-31577923

Links

ENSG00000101294 ∙ NCBI:81502 ∙ OMIM:607106 ∙ HGNC:16435 ∙ Uniprot:Q8TCT9 ∙ 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 HM13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HM13 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						0
missense			27			27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	0	0

Variants in HM13

This is a list of pathogenic ClinVar variants found in the HM13 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-31514570-G-A		not specified	Uncertain significance (Apr 23, 2024)
20-31514576-C-T		not specified	Uncertain significance (Oct 06, 2024)
20-31514583-G-T		not specified	Uncertain significance (Jun 24, 2022)
20-31514592-A-T		not specified	Uncertain significance (May 27, 2022)
20-31514598-G-A		not specified	Uncertain significance (Aug 12, 2024)
20-31514624-C-T		not specified	Uncertain significance (Nov 01, 2022)
20-31514646-T-C		not specified	Uncertain significance (Apr 26, 2023)
20-31514672-C-T		not specified	Uncertain significance (Jun 03, 2022)
20-31527538-A-G		not specified	Uncertain significance (Dec 15, 2023)
20-31538239-C-G		not specified	Uncertain significance (Apr 17, 2024)
20-31544988-G-A		not specified	Uncertain significance (Sep 26, 2023)
20-31545017-T-G		not specified	Uncertain significance (Jul 31, 2023)
20-31545020-G-A		not specified	Uncertain significance (Nov 07, 2022)
20-31549088-G-A		not specified	Uncertain significance (Oct 30, 2023)
20-31549094-G-A		not specified	Uncertain significance (Feb 22, 2023)
20-31549110-G-A		not specified	Uncertain significance (Jan 04, 2022)
20-31554773-A-G		not specified	Uncertain significance (Mar 25, 2024)
20-31566248-T-G		not specified	Uncertain significance (Oct 25, 2023)
20-31566250-C-T		not specified	Uncertain significance (Dec 22, 2023)
20-31566288-A-C		not specified	Uncertain significance (Oct 16, 2023)
20-31568092-C-T		not specified	Uncertain significance (Jul 17, 2024)
20-31568163-G-A		not specified	Uncertain significance (Oct 01, 2024)
20-31568176-A-C		not specified	Uncertain significance (Jan 03, 2024)
20-31568196-C-T		not specified	Uncertain significance (Jul 27, 2024)
20-31568203-G-A		not specified	Uncertain significance (Aug 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HM13	protein_coding	protein_coding	ENST00000398174	13	55140

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.690	0.310	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.09	151	243	0.622	0.0000135	2751
Missense in Polyphen		13	50.048	0.25975		591
Synonymous	1.38	90	108	0.831	0.00000659	873
Loss of Function	3.48	4	21.3	0.188	9.75e-7	243

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000125	0.000122
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000178	0.0000176
Middle Eastern	0.000110	0.000109
South Asian	0.000197	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes intramembrane proteolysis of some signal peptides after they have been cleaved from a preprotein, resulting in the release of the fragment from the ER membrane into the cytoplasm. Required to generate lymphocyte cell surface (HLA-E) epitopes derived from MHC class I signal peptides (PubMed:11714810). May be necessary for the removal of the signal peptide that remains attached to the hepatitis C virus core protein after the initial proteolytic processing of the polyprotein (PubMed:12145199). Involved in the intramembrane cleavage of the integral membrane protein PSEN1 (PubMed:12077416, PubMed:11714810, PubMed:14741365). Cleaves the integral membrane protein XBP1 isoform 1 in a DERL1/RNF139-dependent manner (PubMed:25239945). May play a role in graft rejection (By similarity). {ECO:0000250|UniProtKB:Q9D8V0, ECO:0000269|PubMed:11714810, ECO:0000269|PubMed:12077416, ECO:0000269|PubMed:12145199, ECO:0000269|PubMed:14741365, ECO:0000269|PubMed:25239945}.

Recessive Scores

• pRec: 0.222

Intolerance Scores

• loftool: 0.343
• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.15

Haploinsufficiency Scores

• pHI: 0.294
• hipred: Y
• hipred_score: 0.728
• ghis: 0.511

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.958

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: H13
• Phenotype: homeostasis/metabolism phenotype; craniofacial phenotype; muscle phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; embryo phenotype; renal/urinary system phenotype; skeleton phenotype; immune system phenotype; vision/eye phenotype; limbs/digits/tail phenotype; hearing/vestibular/ear phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); digestive/alimentary phenotype; neoplasm; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); liver/biliary system phenotype; respiratory system phenotype

Gene ontology

• Biological process: signal peptide processing;membrane protein ectodomain proteolysis;membrane protein intracellular domain proteolysis;membrane protein proteolysis;protein homotetramerization;membrane protein proteolysis involved in retrograde protein transport, ER to cytosol
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;rough endoplasmic reticulum;plasma membrane;cell surface;membrane;Derlin-1 retrotranslocation complex;integral component of cytoplasmic side of endoplasmic reticulum membrane;integral component of lumenal side of endoplasmic reticulum membrane
• Molecular function: protein binding;peptidase activity;ubiquitin protein ligase binding;aspartic endopeptidase activity, intramembrane cleaving;protein homodimerization activity