STPG3

protein-coding

sperm-tail PG-rich repeat containing 3

Gene summary

Predicted to be active in cytoskeleton. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C9orf173

MANE transcript

NM_001004353.4

Inheritance

—

ClinVar variants

U:5B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.18

Max pathogenic AF

—

Genomic locus

chr9:137,251,261-137,253,483

External References & Databases

Ensembl (ENSG00000197768)

Transcript & Mutation Effects

hg38 • Region Span ~2.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to STPG3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 3

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001004353.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			4 clinvar	1 clinvar	1 clinvar	6
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	5	1	1	7

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 13 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001004353.4	RefSeq	NP_001004353.2	6	MANE Select
ENST00000412566.6	Ensembl	ENSP00000391218.1	6	MANE Select
NM_001256699.2	RefSeq	NP_001243628.1	6	Standard
NM_001256700.2	RefSeq	NP_001243629.1	6	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000388931
Coding exons: 6
Length: 2222
Individuals with no LoFs: 124552
Homozygous LoFs: 0
Heterozygous LoFs: 51
Defined: 124603
p: 0.000205

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.435	236	218	1.08	0.0000132	2408
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0010	0.00097	notable
Latino/Admixed American	0.00018	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.000094	0.000046	rare
European (Non-Finnish)	0.00017	0.00016	rare
South Asian	0.00027	0.00026	rare
Other	0.00017	0.00017	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: 0.57
RVIS percentile EVS: 82.08