GTSF1

protein-coding

gametocyte specific factor 1

Gene summary

Enables tRNA binding activity. Predicted to be involved in cell differentiation; regulatory ncRNA-mediated gene silencing; and spermatogenesis. Predicted to be located in cytoplasm. Predicted to be active in piP-body. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

FAM112B

MANE transcript

NM_144594.3

Inheritance

—

ClinVar variants

P:2U:13B:1

Top phenotype

Male infertility

gnomAD constraint

pLI —, LoF o/e 0.37

Max pathogenic AF

—

Genomic locus

chr12:54,455,950-54,473,602

External References & Databases

Ensembl (ENSG00000170627)

Transcript & Mutation Effects

hg38 • Region Span ~17.7 kb

Loading mutation effect viewer...

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 GTSF1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 11

not providedTotal: 2

Male infertilityTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_144594.3. 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					1 clinvar	1
missense		1 clinvar	11 clinvar			12
nonsense			1 clinvar			1
start loss						0
frameshift	1 clinvar					1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	1	1	13	0	1	16

Highest pathogenic variant AF is 0.000004959893

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_144594.3	RefSeq	NP_653195.2	7	MANE Select
ENST00000305879.8	Ensembl	ENSP00000304185.5	7	MANE Select
ENST00000546931.5	Ensembl	ENSP00000446918.1	7	Standard
ENST00000552397.5	Ensembl	ENSP00000446485.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

spermatogenesis
cell differentiation

Molecular Function

metal ion binding

Cellular Component

cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000552397
Coding exons: 7
Length: 17653
Individuals with no LoFs: 125736
Homozygous LoFs: 0
Heterozygous LoFs: 10
Defined: 125746
p: 0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.04	63	91.0	0.692	0.00000441	1122
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000088	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000027	0.000026	rare
South Asian	0.000033	0.000033	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.508

Gene Damage Prediction

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