SEMG1

semenogelin 1

Basic information

Region (hg38): 20:45207032-45209768

Previous symbols: [ "SEMG" ]

Links

ENSG00000124233 ∙ NCBI:6406 ∙ OMIM:182140 ∙ HGNC:10742 ∙ Uniprot:P04279 ∙ 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 SEMG1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEMG1 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			33	3		36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	3	0

Variants in SEMG1

This is a list of pathogenic ClinVar variants found in the SEMG1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-45207118-T-C		not specified	Uncertain significance (Feb 14, 2023)
20-45207395-C-T		not specified	Uncertain significance (Dec 01, 2022)
20-45207485-T-C		not specified	Uncertain significance (Feb 06, 2024)
20-45207487-T-C		not specified	Uncertain significance (Dec 17, 2021)
20-45207491-T-C		not specified	Uncertain significance (Aug 08, 2023)
20-45207515-C-T		not specified	Uncertain significance (Jul 26, 2022)
20-45207541-A-C		not specified	Uncertain significance (Jun 03, 2022)
20-45207562-G-A		not specified	Uncertain significance (Mar 23, 2023)
20-45207632-A-G		not specified	Uncertain significance (Jun 29, 2023)
20-45207635-G-A		not specified	Uncertain significance (Sep 14, 2022)
20-45207644-A-G		not specified	Uncertain significance (Dec 31, 2023)
20-45207692-G-A		not specified	Uncertain significance (Jul 19, 2022)
20-45207697-A-C		not specified	Likely benign (Dec 02, 2022)
20-45207740-A-C		not specified	Uncertain significance (Feb 06, 2024)
20-45207811-A-C		not specified	Uncertain significance (May 11, 2022)
20-45207862-G-A		not specified	Uncertain significance (Apr 08, 2022)
20-45207931-A-G		not specified	Uncertain significance (Aug 23, 2021)
20-45207935-C-T		not specified	Uncertain significance (Feb 07, 2023)
20-45207944-A-G		not specified	Uncertain significance (Feb 05, 2024)
20-45207986-A-T		not specified	Uncertain significance (May 18, 2023)
20-45207993-T-A		not specified	Uncertain significance (May 26, 2023)
20-45208052-A-G		not specified	Uncertain significance (Dec 07, 2023)
20-45208101-C-G		not specified	Uncertain significance (Dec 14, 2023)
20-45208129-C-G		not specified	Likely benign (Aug 04, 2021)
20-45208155-A-G		not specified	Uncertain significance (May 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEMG1	protein_coding	protein_coding	ENST00000372781	2	2776

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.357	0.595	125675	0	2	125677	0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.570	265	240	1.10	0.0000118	3055
Missense in Polyphen		109	103.67	1.0514		1449
Synonymous	-1.79	108	86.8	1.24	0.00000417	839
Loss of Function	1.55	1	4.59	0.218	2.81e-7	44

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000546	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000880
Middle Eastern	0.0000546	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Predominant protein in semen. It participates in the formation of a gel matrix entrapping the accessory gland secretions and ejaculated spermatozoa. Fragments of semenogelin and/or fragments of the related proteins may contribute to the activation of progressive sperm movements as the gel-forming proteins are fragmented by KLK3/PSA. {ECO:0000269|PubMed:19889947}.
• Pathway: Antimicrobial peptides;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.946
• rvis_EVS: 0.89
• rvis_percentile_EVS: 89.24

Haploinsufficiency Scores

• pHI: 0.0379
• hipred: N
• hipred_score: 0.133

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.279

Gene Damage Prediction

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

Gene ontology

• Biological process: insemination;antimicrobial humoral response;antibacterial humoral response;killing of cells of other organism;cellular protein metabolic process;sperm capacitation;coagulation;protein heterooligomerization;antimicrobial humoral immune response mediated by antimicrobial peptide;negative regulation of calcium ion import;positive regulation of serine-type endopeptidase activity;negative regulation of flagellated sperm motility
• Cellular component: extracellular region;extracellular space;nucleus;protein-containing complex;extracellular exosome
• Molecular function: protein binding;zinc ion binding