SPATA33

spermatogenesis associated 33

Basic information

Region (hg38): 16:89657740-89671272

Previous symbols: [ "C16orf55" ]

Links

ENSG00000167523 ∙ NCBI:124045 ∙ OMIM:615409 ∙ HGNC:26463 ∙ Uniprot:Q96N06 ∙ 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 SPATA33 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPATA33 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						0
missense			19	1	1	21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	19	1	2

Variants in SPATA33

This is a list of pathogenic ClinVar variants found in the SPATA33 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-89657755-C-A			Likely benign (Sep 18, 2018)
16-89657758-T-C			Likely benign (Jul 05, 2019)
16-89657805-G-T		not specified	Uncertain significance (Jun 01, 2023)
16-89657809-C-T		not specified	Uncertain significance (Oct 06, 2021)
16-89657827-G-C		not specified	Uncertain significance (Sep 28, 2022)
16-89657833-T-C		not specified	Uncertain significance (Dec 07, 2021)
16-89657860-C-T			Benign (Jun 26, 2018)
16-89657905-C-G			Benign (Jun 28, 2018)
16-89658260-A-G		not specified	Uncertain significance (Jun 30, 2023)
16-89658264-G-C		not specified	Uncertain significance (Sep 22, 2023)
16-89658305-T-G		not specified	Uncertain significance (May 17, 2023)
16-89658313-C-T		not specified	Uncertain significance (Jan 11, 2023)
16-89658367-C-T		not specified	Uncertain significance (Aug 11, 2022)
16-89658400-C-T		not specified	Likely benign (Jul 21, 2021)
16-89669314-C-A		not specified	Uncertain significance (Jul 31, 2023)
16-89669341-C-G		not specified	Uncertain significance (May 17, 2023)
16-89669358-C-T		not specified	Uncertain significance (Jan 20, 2023)
16-89669365-G-C		not specified	Uncertain significance (Mar 11, 2024)
16-89669367-C-T		not specified	Uncertain significance (Dec 28, 2022)
16-89669376-G-C		not specified	Uncertain significance (Jan 06, 2023)
16-89669394-G-A		not specified	Uncertain significance (Jan 08, 2024)
16-89669414-C-G		not specified	Uncertain significance (May 08, 2024)
16-89669441-C-T		not specified	Uncertain significance (May 30, 2024)
16-89669442-G-A		not specified	Uncertain significance (Jan 31, 2023)
16-89669444-C-T		not specified	Uncertain significance (Oct 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPATA33	protein_coding	protein_coding	ENST00000301031	3	13471

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000126	0.236	125640	1	104	125745	0.000418

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.13	135	81.1	1.67	0.00000487	903
Missense in Polyphen		45	31.321	1.4367		325
Synonymous	-1.39	46	35.5	1.30	0.00000219	270
Loss of Function	-0.776	5	3.45	1.45	1.44e-7	49

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00549	0.00543
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000980	0.0000980
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.48
• rvis_percentile_EVS: 79.25

Haploinsufficiency Scores

• pHI: 0.0739
• hipred: N
• hipred_score: 0.123
• ghis: 0.409

Essentials

• essential_gene_CRISPR: 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: Spata33

Gene ontology

• Cellular component: nucleus;cytoplasm;cytosol