HMSD

histocompatibility minor serpin domain containing, the group of Minor histocompatibility antigens

Basic information

Region (hg38): 18:63949300-63981774

Previous symbols: [ "C18orf53" ]

Links

ENSG00000221887 ∙ NCBI:284293 ∙ OMIM:612086 ∙ HGNC:23037 ∙ Uniprot:A8MTL9, P0C7T4 ∙ 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 HMSD gene.

• Inborn genetic diseases (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HMSD 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			7	1		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	1	0

Variants in HMSD

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

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

Position	Type	Phenotype	Significance	ClinVar
18-63953476-G-C		not specified	Uncertain significance (Sep 20, 2023)
18-63954442-G-A		not specified	Uncertain significance (Dec 27, 2022)
18-63954451-A-T		not specified	Uncertain significance (Nov 17, 2022)
18-63954457-G-T		not specified	Uncertain significance (Nov 16, 2021)
18-63954466-C-T		not specified	Uncertain significance (Jul 25, 2023)
18-63954477-G-A		not specified	Uncertain significance (Oct 04, 2022)
18-63954493-A-T		not specified	Uncertain significance (Dec 14, 2023)
18-63960198-T-C		not specified	Uncertain significance (Jan 26, 2022)
18-63960243-G-A		not specified	Likely benign (Sep 27, 2022)
18-63960318-G-T		not specified	Uncertain significance (Jun 11, 2021)
18-63978310-T-C		Peeling skin syndrome 5	Pathogenic (Sep 13, 2016)
18-63978343-C-G		not specified	Uncertain significance (Feb 14, 2023)
18-63978389-C-T			Benign (Oct 07, 2023)
18-63978394-T-C			Benign (Aug 31, 2023)
18-63978438-A-G		not specified	Uncertain significance (Dec 27, 2023)
18-63979829-T-C		not specified	Uncertain significance (Jun 29, 2022)
18-63979835-G-A		Peeling skin syndrome 5	Benign (Jan 29, 2024)
18-63979886-T-G			Benign (Jan 04, 2024)
18-63979901-AC-A		Peeling skin syndrome 5	Likely pathogenic (-)
18-63979920-G-C		not specified	Uncertain significance (Jul 28, 2021)
18-63979936-C-T			Likely benign (Dec 15, 2022)
18-63980032-C-T			Benign (May 14, 2021)
18-63980245-A-T			Benign (Jun 19, 2021)
18-63981491-C-T			Benign (May 22, 2021)
18-63981603-G-A			Benign (May 22, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HMSD	protein_coding	protein_coding	ENST00000408945	3	32474

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0129	0.674	124787	0	3	124790	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.584	60	74.2	0.809	0.00000375	919
Missense in Polyphen		15	20.225	0.74166		271
Synonymous	-0.334	27	24.9	1.08	0.00000137	254
Loss of Function	0.540	3	4.19	0.715	2.44e-7	46

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000647	0.0000646
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000178	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative serine protease inhibitor. {ECO:0000250}.

Intolerance Scores

• loftool: 0.503
• rvis_EVS: -0.08
• rvis_percentile_EVS: 47.79

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.180
• ghis: 0.636

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.178

Gene Damage Prediction

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

Gene ontology

• Biological process: activation of immune response;negative regulation of endopeptidase activity
• Cellular component: extracellular space
• Molecular function: serine-type endopeptidase inhibitor activity