TOPAZ1

testis and ovary specific TOPAZ 1

Basic information

Region (hg38): 3:44241885-44332098

Previous symbols: [ "C3orf77" ]

Links

ENSG00000173769 ∙ NCBI:375337 ∙ OMIM:614412 ∙ HGNC:24746 ∙ Uniprot:Q8N9V7 ∙ 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 TOPAZ1 gene.

• Inborn genetic diseases (59 variants)
• not provided (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TOPAZ1 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					2	2
missense			53	5	4	62
nonsense						0
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	53	5	7

Variants in TOPAZ1

This is a list of pathogenic ClinVar variants found in the TOPAZ1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-44242082-C-G		not specified	Uncertain significance (Sep 16, 2021)
3-44242133-C-T		not specified	Uncertain significance (Dec 07, 2023)
3-44242151-C-T		not specified	Uncertain significance (Sep 22, 2023)
3-44242174-G-A		not specified	Uncertain significance (Jan 23, 2023)
3-44242222-A-C		not specified	Uncertain significance (Jul 27, 2021)
3-44242237-G-A		not specified	Uncertain significance (Jan 12, 2024)
3-44242285-G-A		not specified	Uncertain significance (Jul 13, 2021)
3-44242333-T-TCGTCAGACC			Benign (Dec 31, 2019)
3-44242337-C-T		not specified	Uncertain significance (Jun 07, 2023)
3-44242376-T-G		not specified	Uncertain significance (Jun 16, 2023)
3-44242381-T-G		not specified	Uncertain significance (Sep 26, 2023)
3-44242388-C-T		not specified	Uncertain significance (Apr 27, 2022)
3-44242860-A-C		not specified	Uncertain significance (Dec 30, 2023)
3-44242993-A-C		not specified	Uncertain significance (Dec 27, 2023)
3-44243104-G-A		not specified	Uncertain significance (Aug 12, 2021)
3-44243143-A-G		not specified	Uncertain significance (Dec 19, 2023)
3-44243152-C-A		not specified	Uncertain significance (Mar 01, 2024)
3-44243202-C-G		not specified	Uncertain significance (Jan 17, 2024)
3-44243272-G-A		not specified	Uncertain significance (Apr 10, 2023)
3-44243299-C-T		not specified	Likely benign (Apr 07, 2022)
3-44243363-A-G		not specified	Uncertain significance (Oct 06, 2021)
3-44243486-G-A		not specified	Uncertain significance (May 01, 2022)
3-44243489-G-A		not specified	Uncertain significance (Jun 09, 2022)
3-44243505-G-C		not specified	Uncertain significance (Nov 07, 2022)
3-44243621-C-T		not specified	Uncertain significance (Dec 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TOPAZ1	protein_coding	protein_coding	ENST00000309765	20	90213

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.977	0.0225	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.90	600	746	0.804	0.0000377	11131
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Topaz1
• Phenotype: reproductive system phenotype; endocrine/exocrine gland phenotype; cellular phenotype

Gene ontology

• Biological process: apoptotic process;spermatid development;spermatocyte division;ncRNA transcription;positive regulation of meiotic cell cycle phase transition
• Cellular component: cytosol