MSMP

microseminoprotein, prostate associated

Basic information

Region (hg38): 9:35752990-35756613

Links

ENSG00000215183 ∙ NCBI:692094 ∙ OMIM:612191 ∙ HGNC:29663 ∙ Uniprot:Q1L6U9 ∙ 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 MSMP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MSMP 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in MSMP

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

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

Position	Type	Phenotype	Significance	ClinVar
9-35753167-C-G		not specified	Uncertain significance (May 23, 2024)
9-35753188-C-T		not specified	Uncertain significance (Dec 21, 2023)
9-35753239-C-T		not specified	Uncertain significance (Dec 16, 2023)
9-35753257-G-A		not specified	Uncertain significance (Oct 12, 2021)
9-35754026-T-C		not specified	Uncertain significance (Apr 27, 2024)
9-35754065-C-A		not specified	Uncertain significance (Jun 10, 2024)
9-35754081-C-A		not specified	Uncertain significance (Dec 12, 2023)
9-35754126-C-T		not specified	Uncertain significance (Mar 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MSMP	protein_coding	protein_coding	ENST00000436428	3	3624

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0484	0.866	124789	0	8	124797	0.0000321

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0587	79	80.5	0.982	0.00000420	894
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000195	0.000194
Ashkenazi Jewish	0.0000994	0.0000993
East Asian	0.0000556	0.0000556
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000556	0.0000556
South Asian	0.0000654	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.563
• rvis_EVS: 0.37
• rvis_percentile_EVS: 74.95

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.329

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.382

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Msmp

Gene ontology

• Biological process: biological_process
• Cellular component: extracellular space;cytoplasm
• Molecular function: molecular_function