TOPAZ1

protein-coding

testis and ovary specific TOPAZ 1

Gene summary

Predicted to be involved in spermatocyte division. Predicted to act upstream of or within apoptotic process and lncRNA transcription. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C3orf77

MANE transcript

NM_001145030.2

Inheritance

—

ClinVar variants

U:224B:27

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.19

Max pathogenic AF

—

Genomic locus

chr3:44,241,886-44,332,098

External References & Databases

Ensembl (ENSG00000173769)

Transcript & Mutation Effects

hg38 • Region Span ~90.2 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 TOPAZ1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 244

not providedTotal: 8

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001145030.2. 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					2 clinvar	2
missense			224 clinvar	21 clinvar	4 clinvar	249
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	224	21	6	251

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001145030.2	RefSeq	NP_001138502.1	20	MANE Select
ENST00000309765.4	Ensembl	ENSP00000310303.4	20	MANE Select
XM_011533694.3	RefSeq	XP_011531996.1	20	Standard
XM_017006361.2	RefSeq	XP_016861850.1	18	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

apoptotic process
spermatid development
spermatocyte division
ncRNA transcription
positive regulation of meiotic cell cycle phase transition

Cellular Component

cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000309765
Coding exons: 20
Length: 90213
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.90	600	746	0.804	0.0000377	11131
Missense (PolyPhen)		104	196.74	0.52861		3395
Synonymous	1.71	235	271	0.867	0.0000142	3097
Loss of Function	6.06	12	64.5	0.186	0.00000366	1030

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Important for normal spermatogenesis and male fertility. Specifically required for progression to the post-meiotic stages of spermatocyte development. Seems to be necessary for normal expression levels of a number of testis-expressed gene transcripts, although its role in this process is unclear. {ECO:0000250|UniProtKB:E5FYH1}.;

Intolerance Scores

RVIS EVS: 3.04
RVIS percentile EVS: 99.23

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