STPG1

protein-coding

sperm tail PG-rich repeat containing 1

Gene summary

Involved in positive regulation of apoptotic process and positive regulation of mitochondrial membrane permeability involved in apoptotic process. Predicted to be located in mitochondrion and nucleus. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C1orf201

MANE transcript

NM_001199013.2

Inheritance

—

ClinVar variants

U:62B:5

Top phenotype

Van der Woude syndrome 2

gnomAD constraint

pLI —, LoF o/e 0.87

Max pathogenic AF

—

Genomic locus

chr1:24,356,999-24,416,934

External References & Databases

Ensembl (ENSG00000001460)

Transcript & Mutation Effects

hg38 • Region Span ~59.9 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 STPG1 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 65

Van der Woude syndrome 2Total: 9

not providedTotal: 4

GRHL3-related disorderTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001199013.2. 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			1 clinvar	1 clinvar		2
missense			60 clinvar	4 clinvar		64
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	62	5	0	67

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 26 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001199013.2	RefSeq	NP_001185942.1	8	MANE Select
ENST00000337248.9	Ensembl	ENSP00000337461.4	8	MANE Select
NM_001199012.2	RefSeq	NP_001185941.1	8	Standard
NM_001199014.2	RefSeq	NP_001185943.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

positive regulation of apoptotic process
positive regulation of protein homodimerization activity
positive regulation of mitochondrial membrane permeability involved in apoptotic process

Molecular Function

molecular_function

Cellular Component

nucleus
mitochondrion

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000374409
Coding exons: 8
Length: 59936
Individuals with no LoFs: 125614
Homozygous LoFs: 1
Heterozygous LoFs: 133
Defined: 125748
p: 0.000533

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.250	183	193	0.949	0.0000111	2162
Missense (PolyPhen)		60	59.571	1.0072		656
Synonymous	0.548	71	77.1	0.921	0.00000510	644
Loss of Function	0.502	15	17.2	0.870	9.71e-7	206

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00018	0.00018	rare
Latino/Admixed American	0.00014	0.00014	rare
Ashkenazi Jewish	0.00020	0.000099	rare
East Asian	0.0056	0.0055	notable
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0.00042	0.00036	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May positively contribute to the induction of apoptosis triggered by O(6)-methylguanine. {ECO:0000269|PubMed:23028632}.;

Intolerance Scores

RVIS EVS: 0.42
RVIS percentile EVS: 77.06

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium