STPG3

sperm-tail PG-rich repeat containing 3

Basic information

Region (hg38): 9:137251261-137253483

Previous symbols: [ "C9orf173" ]

Links

ENSG00000197768NCBI:441476HGNC:37285Uniprot:Q8N7X2AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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
clinvar
1
missense
2
clinvar
1
clinvar
1
clinvar
4
nonsense
0
start loss
0
frameshift
1
clinvar
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)2204269
9-137252108-A-G Benign (Jun 16, 2018)774890
9-137252481-G-A not specified Uncertain significance (May 20, 2024)2261888
9-137253150-G-C not specified Uncertain significance (Sep 01, 2021)2248722
9-137253271-C-A Likely benign (Sep 01, 2022)2659816
9-137253370-GATGCACCCTTCTGGCTGGCCAACCCTTCT-G Benign (Oct 10, 2019)732859

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
STPG3protein_codingprotein_codingENST00000388931 62222
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
9.12e-130.01091245520511246030.000205
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.4352362181.080.00001322408
Missense in Polyphen105101.321.03631091
Synonymous-0.50110295.81.070.00000617808
Loss of Function-0.6201714.51.188.02e-7142

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001190.00115
Ashkenazi Jewish0.000.00
East Asian0.0001110.000111
Finnish0.00009400.0000464
European (Non-Finnish)0.0001700.000159
Middle Eastern0.0001110.000111
South Asian0.0002660.000261
Other0.0001660.000165

dbNSFP

Source: dbNSFP

Intolerance Scores

loftool
rvis_EVS
0.57
rvis_percentile_EVS
82.08

Haploinsufficiency Scores

pHI
hipred
N
hipred_score
0.123
ghis
0.414

Mouse Genome Informatics

Gene name
Stpg3
Phenotype