STPG1

sperm tail PG-rich repeat containing 1

Basic information

Region (hg38): 1:24356999-24416934

Previous symbols: [ "C1orf201" ]

Links

ENSG00000001460 ∙ NCBI:90529 ∙ OMIM:615826 ∙ HGNC:28070 ∙ Uniprot:Q5TH74 ∙ 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 STPG1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STPG1 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			26	2		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2		6	8
Total	0	0	28	2	6

Variants in STPG1

This is a list of pathogenic ClinVar variants found in the STPG1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-24360877-G-A		not specified	Uncertain significance (Mar 18, 2024)
1-24360881-C-T			Likely benign (Sep 01, 2024)
1-24360883-G-A		not specified	Uncertain significance (Jan 21, 2025)
1-24360892-C-T		not specified	Uncertain significance (Oct 02, 2023)
1-24360901-T-C		not specified	Uncertain significance (Oct 27, 2023)
1-24360902-T-C		not specified	Uncertain significance (Aug 20, 2024)
1-24360931-T-C		not specified	Uncertain significance (Sep 16, 2021)
1-24360938-G-A		not specified	Uncertain significance (Jul 14, 2021)
1-24360956-C-T		not specified	Uncertain significance (Aug 02, 2024)
1-24363924-A-G			Benign (Nov 12, 2018)
1-24364186-G-A		not specified • Van der Woude syndrome 2 • GRHL3-related disorder	Benign (Jan 30, 2025)
1-24364202-A-T		Van der Woude syndrome 2	Likely benign (Oct 15, 2024)
1-24364208-G-A		Van der Woude syndrome 2 • GRHL3-related disorder	Benign/Likely benign (Apr 01, 2025)
1-24364216-C-T		Van der Woude syndrome 2	Uncertain significance (Jun 27, 2022)
1-24364225-C-T		GRHL3-related disorder	Uncertain significance (Mar 27, 2024)
1-24364250-A-C		Van der Woude syndrome 2	Uncertain significance (Oct 22, 2024)
1-24364257-G-A		Van der Woude syndrome 2	Conflicting classifications of pathogenicity (Jul 22, 2024)
1-24364274-T-A		Van der Woude syndrome 2	Benign (Jan 29, 2025)
1-24364296-G-A		Van der Woude syndrome 2	Uncertain significance (Mar 06, 2020)
1-24364326-C-A		Van der Woude syndrome 2	Uncertain significance (Sep 23, 2022)
1-24364347-G-A		GRHL3-related disorder	Likely benign (Mar 08, 2022)
1-24364404-C-T			Benign (Nov 12, 2018)
1-24364647-T-C			Benign (Nov 12, 2018)
1-24369678-A-G		not specified	Uncertain significance (Jul 05, 2024)
1-24369710-C-T		not specified	Likely benign (Feb 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STPG1	protein_coding	protein_coding	ENST00000374409	8	59936

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.20e-9	0.188	125614	1	133	125748	0.000533

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.250	183	193	0.949	0.0000111	2162
Missense in Polyphen		60	59.571	1.0072		656
Synonymous	0.548	71	77.1	0.921	0.00000510	644
Loss of Function	0.502	15	17.2	0.870	9.71e-7	206

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000330	0.000329
Ashkenazi Jewish	0.000200	0.0000992
East Asian	0.00555	0.00545
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.00555	0.00545
South Asian	0.000416	0.000359
Other	0.000171	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May positively contribute to the induction of apoptosis triggered by O(6)-methylguanine. {ECO:0000269|PubMed:23028632}.

Intolerance Scores

• rvis_EVS: 0.42
• rvis_percentile_EVS: 77.06

Haploinsufficiency Scores

• pHI: 0.0787
• hipred: N
• hipred_score: 0.146
• ghis: 0.475

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stpg1

Gene ontology

• Biological process: positive regulation of apoptotic process;positive regulation of protein homodimerization activity;positive regulation of mitochondrial membrane permeability involved in apoptotic process
• Cellular component: nucleus;mitochondrion
• Molecular function: molecular_function