SPATA24

spermatogenesis associated 24

Basic information

Region (hg38): 5:139396563-139404089

Links

ENSG00000170469

∙ NCBI:202051 ∙ ∙ HGNC:27322 ∙ Uniprot:Q86W54 ∙ 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 SPATA24 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPATA24 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			2 clinvar			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	0	0

Variants in SPATA24

This is a list of pathogenic ClinVar variants found in the SPATA24 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-139401961-C-T		not specified	Uncertain significance (Nov 15, 2021)	2261294
5-139402682-C-G		not specified	Uncertain significance (Aug 09, 2021)	2241576

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPATA24	protein_coding	protein_coding	ENST00000450845	6	7526

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00262	0.940	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.21	73	108	0.674	0.00000538	1361
Missense in Polyphen		25	32.06	0.77979		447
Synonymous	2.31	23	42.1	0.547	0.00000200	353
Loss of Function	1.66	6	12.3	0.489	6.12e-7	140

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: Binds DNA with high affinity but does not bind to TATA boxes. Synergises with GMNN and TBP in activation of TATA box- containing promoters and with GMNN and TBPL1 in activation of the NF1 TATA-less promoter. May play a role in cytoplasm movement and removal during spermiogenesis (By similarity). {ECO:0000250}.;

Intolerance Scores

loftool
rvis_EVS: 0.48
rvis_percentile_EVS: 78.95

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Spata24
Phenotype

Gene ontology

Biological process: multicellular organism development;spermatogenesis;cell differentiation
Cellular component: nucleus;nucleoplasm;nucleolus;cytosol
Molecular function: DNA binding;protein binding;protein homodimerization activity