GTSF1

gametocyte specific factor 1

Basic information

Region (hg38): 12:54455949-54473602

Previous symbols: [ "FAM112B" ]

Links

ENSG00000170627 ∙ NCBI:121355 ∙ OMIM:617484 ∙ HGNC:26565 ∙ Uniprot:Q8WW33 ∙ 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 GTSF1 gene.

• Male infertility (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GTSF1 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	1
missense		1	2			3
nonsense						0
start loss						0
frameshift	1					1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	1	1	2	0	2

Variants in GTSF1

This is a list of pathogenic ClinVar variants found in the GTSF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-54460400-G-A		not specified	Uncertain significance (Oct 04, 2022)
12-54462153-G-A			Benign (Oct 19, 2017)
12-54462182-G-A			Benign (Oct 19, 2017)
12-54463192-TTC-T		Male infertility	Pathogenic (Feb 27, 2023)
12-54465072-T-C		not specified	Uncertain significance (Nov 09, 2021)
12-54465087-G-T		Male infertility	Likely pathogenic (Feb 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GTSF1	protein_coding	protein_coding	ENST00000552397	7	17653

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0221	0.964	125736	0	10	125746	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.04	63	91.0	0.692	0.00000441	1122
Missense in Polyphen		10	21.106	0.47379		289
Synonymous	-0.880	37	30.8	1.20	0.00000158	283
Loss of Function	2.15	5	13.5	0.370	7.03e-7	141

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000884	0.0000884
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000267	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for spermatogenesis and is involved in the suppression of retrotransposon transcription in male germ cells. {ECO:0000250|UniProtKB:Q9DAN6}.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.386
• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.54

Haploinsufficiency Scores

• pHI: 0.478
• hipred: N
• hipred_score: 0.484
• ghis: 0.464

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.508

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gtsf1
• Phenotype: endocrine/exocrine gland phenotype; cellular phenotype; reproductive system phenotype

Gene ontology

• Biological process: spermatogenesis;cell differentiation
• Cellular component: cytoplasm
• Molecular function: metal ion binding