HMSD

protein-coding

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

Gene summary

This gene encodes a serpin-domain containing protein that may function as a serine protease inhibitor. This gene is primarily expressed in cells of myeloid lineage. A polymorphism in this gene may result in the expression a splice variant that encodes a minor histocompatibility antigen. [provided by RefSeq, Oct 2010]

Previous symbols:

C18orf53

MANE transcript

NM_001123366.2

Inheritance

—

ClinVar variants

U:21B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.72

Max pathogenic AF

—

Genomic locus

chr18:63,949,301-63,981,774

External References & Databases

Ensembl (ENSG00000221887)

UniProt (A8MTL9, P0C7T4)

Transcript & Mutation Effects

hg38 • Region Span ~32.5 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to HMSD variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 23

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001123366.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			21 clinvar	2 clinvar		23
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	21	2	0	23

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001123366.2	RefSeq	NP_001116838.1	3	MANE Select
ENST00000408945.5	Ensembl	ENSP00000386207.3	3	MANE Select
ENST00000526932.1	Ensembl	ENSP00000431632.1	2	Standard
ENST00001132574.1	Ensembl	ENSP00000812374.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

activation of immune response
negative regulation of endopeptidase activity

Molecular Function

serine-type endopeptidase inhibitor activity

Cellular Component

extracellular space

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000408945
Coding exons: 3
Length: 32474
Individuals with no LoFs: 124787
Homozygous LoFs: 0
Heterozygous LoFs: 3
Defined: 124790
p: 0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.584	60	74.2	0.809	0.00000375	919
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000065	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

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

Intolerance Scores

LoFtool: 0.503
RVIS EVS: -0.08
RVIS percentile EVS: 47.79

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.178

Gene Damage Prediction

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