STPG3

sperm-tail PG-rich repeat containing 3

Basic information

Region (hg38): 9:137251261-137253483

Previous symbols: [ "C9orf173" ]

Links

ENSG00000197768 ∙ NCBI:441476 ∙ ∙ HGNC:37285 ∙ Uniprot:Q8N7X2 ∙ 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 STPG3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STPG3 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				1		1
missense			2	1	1	4
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	2	2

Variants in STPG3

This is a list of pathogenic ClinVar variants found in the STPG3 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-137251863-T-C		not specified	Likely benign (Aug 02, 2021)
9-137252108-A-G			Benign (Jun 16, 2018)
9-137252481-G-A		not specified	Uncertain significance (May 20, 2024)
9-137253150-G-C		not specified	Uncertain significance (Sep 01, 2021)
9-137253271-C-A			Likely benign (Sep 01, 2022)
9-137253370-GATGCACCCTTCTGGCTGGCCAACCCTTCT-G			Benign (Oct 10, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STPG3	protein_coding	protein_coding	ENST00000388931	6	2222

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.12e-13	0.0109	124552	0	51	124603	0.000205

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.435	236	218	1.08	0.0000132	2408
Missense in Polyphen		105	101.32	1.0363		1091
Synonymous	-0.501	102	95.8	1.07	0.00000617	808
Loss of Function	-0.620	17	14.5	1.18	8.02e-7	142

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00119	0.00115
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000111
Finnish	0.0000940	0.0000464
European (Non-Finnish)	0.000170	0.000159
Middle Eastern	0.000111	0.000111
South Asian	0.000266	0.000261
Other	0.000166	0.000165

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.57
• rvis_percentile_EVS: 82.08

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123
• ghis: 0.414

Mouse Genome Informatics

• Gene name: Stpg3