STPG2

sperm tail PG-rich repeat containing 2

Basic information

Region (hg38): 4:97184092-98143476

Previous symbols: [ "C4orf37" ]

Links

ENSG00000163116 ∙ NCBI:285555 ∙ ∙ HGNC:28712 ∙ Uniprot:Q8N412 ∙ 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 STPG2 gene.

• Inborn genetic diseases (26 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STPG2 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			23	3		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	4	0

Variants in STPG2

This is a list of pathogenic ClinVar variants found in the STPG2 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-97559081-C-T		not specified	Likely benign (Apr 27, 2022)
4-97559104-T-C		not specified	Uncertain significance (May 15, 2023)
4-97712746-G-A		not specified	Uncertain significance (Jan 31, 2022)
4-97840853-C-T		not specified	Uncertain significance (Aug 02, 2021)
4-97840856-G-A		not specified	Uncertain significance (Aug 10, 2021)
4-97943898-A-G		not specified	Uncertain significance (Jan 18, 2022)
4-97943946-T-C		not specified	Uncertain significance (May 25, 2022)
4-97943947-A-G		not specified	Uncertain significance (Sep 07, 2022)
4-97943988-C-T		not specified	Uncertain significance (Dec 07, 2021)
4-97972300-G-C		not specified	Uncertain significance (Dec 15, 2022)
4-97972321-G-T		not specified	Uncertain significance (Aug 12, 2021)
4-97972326-G-A		not specified	Likely benign (Sep 16, 2021)
4-97972339-G-A		not specified	Uncertain significance (Apr 07, 2022)
4-97972385-G-C		not specified	Uncertain significance (Mar 27, 2023)
4-97981194-C-T		not specified	Uncertain significance (Jan 04, 2022)
4-97981216-G-T		not specified	Uncertain significance (Feb 16, 2023)
4-97981258-C-T		not specified	Uncertain significance (Jan 31, 2024)
4-97981263-C-T		not specified	Uncertain significance (Jul 19, 2023)
4-97981264-G-C		not specified	Uncertain significance (May 18, 2023)
4-97981290-G-A		not specified	Uncertain significance (Aug 23, 2021)
4-98105961-T-C		not specified	Likely benign (Dec 01, 2022)
4-98106034-G-A			Likely benign (Dec 01, 2022)
4-98109262-C-T		not specified	Uncertain significance (May 25, 2023)
4-98128451-G-T		not specified	Uncertain significance (Jul 14, 2023)
4-98128471-G-C		not specified	Uncertain significance (Jan 31, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STPG2	protein_coding	protein_coding	ENST00000295268	11	959148

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.33e-17	0.00481	125727	0	21	125748	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.496	254	233	1.09	0.0000109	2948
Missense in Polyphen		69	72.43	0.95265		846
Synonymous	-0.412	83	78.4	1.06	0.00000354	880
Loss of Function	-0.203	24	23.0	1.05	0.00000119	313

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000222	0.000222
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000123	0.000114
Middle Eastern	0.00	0.00
South Asian	0.0000656	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 1.22
• rvis_percentile_EVS: 93.21

Haploinsufficiency Scores

• pHI: 0.136
• hipred: N
• hipred_score: 0.146

Essentials

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

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Stpg2