STPG4

sperm-tail PG-rich repeat containing 4

Basic information

Region (hg38): 2:47045538-47155308

Previous symbols: [ "C2orf61" ]

Links

ENSG00000239605 ∙ NCBI:285051 ∙ ∙ HGNC:26850 ∙ Uniprot:Q8N801 ∙ 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 STPG4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STPG4 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			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	0	0

Variants in STPG4

This is a list of pathogenic ClinVar variants found in the STPG4 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-47046298-A-G		Multiple gastrointestinal atresias	Likely benign (Jun 15, 2022)
2-47046303-C-A		Multiple gastrointestinal atresias	Likely benign (Jul 14, 2023)
2-47046304-C-T		Multiple gastrointestinal atresias	Likely benign (Jan 06, 2024)
2-47046305-G-A		Multiple gastrointestinal atresias	Likely benign (Jan 11, 2024)
2-47046305-G-C		Multiple gastrointestinal atresias	Likely benign (Oct 08, 2020)
2-47046309-C-A		TTC7A-related disorder	Likely benign (May 30, 2019)
2-47046315-C-G		Inborn genetic diseases	Uncertain significance (Feb 05, 2024)
2-47046316-C-T		Multiple gastrointestinal atresias	Likely benign (Aug 09, 2022)
2-47046318-G-A		Multiple gastrointestinal atresias	Likely benign (May 22, 2023)
2-47046319-A-G		Multiple gastrointestinal atresias	Uncertain significance (Mar 05, 2020)
2-47046320-T-C		Multiple gastrointestinal atresias	Uncertain significance (Jun 28, 2022)
2-47046329-A-G		Multiple gastrointestinal atresias • not specified • Gastrointestinal defects and immunodeficiency syndrome 1 • TTC7A-related disorder	Conflicting classifications of pathogenicity (Jan 25, 2024)
2-47046331-G-A		Multiple gastrointestinal atresias	Uncertain significance (Oct 25, 2022)
2-47046336-G-A		Multiple gastrointestinal atresias	Likely benign (Jan 28, 2023)
2-47046348-G-A		Multiple gastrointestinal atresias	Likely benign (Dec 11, 2019)
2-47046351-G-A		Multiple gastrointestinal atresias	Likely benign (Jun 19, 2021)
2-47046354-A-G		Multiple gastrointestinal atresias	Likely benign (Jan 19, 2024)
2-47046356-G-T		Multiple gastrointestinal atresias	Uncertain significance (Nov 28, 2022)
2-47046361-G-C		Multiple gastrointestinal atresias	Uncertain significance (Aug 31, 2022)
2-47046369-C-T		Multiple gastrointestinal atresias	Likely benign (Jun 30, 2022)
2-47046371-T-C		Multiple gastrointestinal atresias	Uncertain significance (Apr 29, 2021)
2-47046372-C-T		Multiple gastrointestinal atresias • TTC7A-related disorder	Benign (Jan 31, 2024)
2-47046373-G-A		Multiple gastrointestinal atresias	Uncertain significance (Jul 20, 2022)
2-47046373-G-C		Multiple gastrointestinal atresias	Uncertain significance (Feb 10, 2022)
2-47046375-G-T		Multiple gastrointestinal atresias	Likely benign (Aug 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STPG4	protein_coding	protein_coding	ENST00000445927	7	109841

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000951	0.809	125720	0	27	125747	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.861	162	134	1.21	0.00000686	1600
Missense in Polyphen		61	53.366	1.143		619
Synonymous	-1.39	61	48.6	1.25	0.00000266	485
Loss of Function	1.21	8	12.6	0.633	5.97e-7	163

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000182	0.000182
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000176	0.000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Maternal factor that plays a role in epigenetic chromatin reprogramming during early development of the zygote. Involved in the regulation of gametic DNA demethylation by inducing the conversion of the modified genomic base 5- methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC). {ECO:0000250|UniProtKB:Q9DAG5}.

Intolerance Scores

• rvis_EVS: 1.19
• rvis_percentile_EVS: 92.89

Haploinsufficiency Scores

• pHI: 0.199
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Stpg4
• Phenotype: normal phenotype

Gene ontology

• Biological process: chromatin organization;DNA demethylation of male pronucleus;C-5 methylation of cytosine;positive regulation of DNA demethylation
• Cellular component: female pronucleus;male pronucleus;nucleus;cytoplasm;germinal vesicle
• Molecular function: chromatin binding;histone binding