STPG2

Gene

sperm tail PG-rich repeat containing 2

Gene summary

No gene description available in the current model. Review primary literature for detailed gene function and characteristics.

Previous symbols:

C4orf37

MANE transcript

NM_174952.3

Inheritance

—

ClinVar variants

U:71B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.05

Max pathogenic AF

—

Genomic locus

chr4:97,184,093-98,143,476

External References & Databases

Ensembl (ENSG00000163116)

Transcript & Mutation Effects

hg38 • Region Span ~959.4 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 STPG2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 70

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_174952.3. 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			2 clinvar	1 clinvar		3
missense			66 clinvar	4 clinvar		70
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	71	5	0	76

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_174952.3	RefSeq	NP_777612.1	11	MANE Select
ENST00000295268.4	Ensembl	ENSP00000295268.3	11	MANE Select
ENST00000522676.5	Ensembl	ENSP00000428346.1	5	Standard
ENST00001137624.1	Ensembl	ENSP00000804997.1	11	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000295268
Coding exons: 11
Length: 959148
Individuals with no LoFs: 125727
Homozygous LoFs: 0
Heterozygous LoFs: 21
Defined: 125748
p: 0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.496	254	233	1.09	0.0000109	2948
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00016	0.00014	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00012	0.00011	rare
South Asian	0.000066	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: 1.22
RVIS percentile EVS: 93.21

Essentials

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

Gene Damage Prediction

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