MSMP

protein-coding

microseminoprotein, prostate associated

Gene summary

This gene encodes a member of the beta-microseminoprotein family. Members of this protein family contain ten conserved cysteine residues that form intra-molecular disulfide bonds. The encoded protein may play a role in prostate cancer tumorigenesis. [provided by RefSeq, Jan 2011]

MANE transcript

NM_001044264.3

Inheritance

—

ClinVar variants

U:18

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.42

Max pathogenic AF

—

Genomic locus

chr9:35,752,990-35,756,613

External References & Databases

Ensembl (ENSG00000215183)

Transcript & Mutation Effects

hg38 • Region Span ~3.6 kb

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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 MSMP variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 16

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001044264.3. 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			1 clinvar			1
missense			16 clinvar			16
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	18	0	0	18

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001044264.3	RefSeq	NP_001037729.1	3	MANE Select
ENST00000436428.3	Ensembl	ENSP00000419194.1	3	MANE Select
ENST00001140210.1	Ensembl	ENSP00000813398.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biological_process

Molecular Function

molecular_function

Cellular Component

extracellular space
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000436428
Coding exons: 3
Length: 3624
Individuals with no LoFs: 124789
Homozygous LoFs: 0
Heterozygous LoFs: 8
Defined: 124797
p: 0.0000321

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0587	79	80.5	0.982	0.00000420	894
Missense (PolyPhen)		27	32.024	0.84312		369
Synonymous	0.335	28	30.3	0.923	0.00000154	281
Loss of Function	1.42	3	7.07	0.424	3.94e-7	75

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00019	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.000056	0.000056	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0	0.0	absent
South Asian	0.000065	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.563
RVIS EVS: 0.37
RVIS percentile EVS: 74.95

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.382

Gene Damage Prediction

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