SPATA19

spermatogenesis associated 19

Basic information

Region (hg38): 11:133840631-133845538

Links

ENSG00000166118 ∙ NCBI:219938 ∙ OMIM:609805 ∙ HGNC:30614 ∙ Uniprot:Q7Z5L4 ∙ 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 SPATA19 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPATA19 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	2		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	2	0

Variants in SPATA19

This is a list of pathogenic ClinVar variants found in the SPATA19 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-133842055-G-A		not specified	Uncertain significance (Dec 20, 2022)
11-133842059-G-T		not specified	Uncertain significance (Apr 13, 2023)
11-133842061-C-G		not specified	Uncertain significance (Aug 05, 2024)
11-133842061-C-T		not specified	Uncertain significance (Dec 27, 2023)
11-133842091-G-A		not specified	Uncertain significance (Mar 20, 2024)
11-133842097-C-T		not specified	Likely benign (Aug 09, 2021)
11-133842494-A-G		not specified	Uncertain significance (Oct 06, 2024)
11-133842515-A-G		not specified	Uncertain significance (Feb 06, 2024)
11-133842554-C-T		not specified	Uncertain significance (Mar 29, 2023)
11-133844253-T-C		not specified	Uncertain significance (Feb 28, 2024)
11-133844261-T-G		not specified	Uncertain significance (Feb 14, 2025)
11-133844268-G-C		not specified	Uncertain significance (Jun 07, 2024)
11-133844300-T-A		not specified	Uncertain significance (Mar 22, 2023)
11-133844304-C-T		not specified	Uncertain significance (Sep 27, 2024)
11-133844334-T-C		not specified	Uncertain significance (Feb 22, 2025)
11-133844511-C-T		not specified	Uncertain significance (Nov 09, 2022)
11-133844539-A-C		not specified	Uncertain significance (Apr 06, 2023)
11-133844544-T-G		not specified	Uncertain significance (Dec 12, 2024)
11-133844549-G-A		not specified	Uncertain significance (Apr 04, 2024)
11-133844562-A-G		not specified	Uncertain significance (Dec 28, 2023)
11-133844564-A-G		not specified	Uncertain significance (Apr 20, 2024)
11-133845149-A-T		not specified	Likely benign (Sep 27, 2022)
11-133845189-T-A		not specified	Uncertain significance (Jan 02, 2024)
11-133845436-G-A		not specified	Uncertain significance (Jul 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPATA19	protein_coding	protein_coding	ENST00000299140	6	4908

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.51e-8	0.191	125690	1	57	125748	0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.281	108	100	1.08	0.00000554	1100
Missense in Polyphen		22	18.61	1.1822		160
Synonymous	-0.212	34	32.5	1.05	0.00000166	317
Loss of Function	0.255	12	13.0	0.924	9.03e-7	115

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000732	0.000731
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000272	0.000272
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000203	0.000202
Middle Eastern	0.000272	0.000272
South Asian	0.000398	0.000359
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May have a role in spermiogenesis.

Recessive Scores

• pRec: 0.0793

Intolerance Scores

• loftool: 0.821
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.76

Haploinsufficiency Scores

• pHI: 0.0619
• hipred: N
• hipred_score: 0.123
• ghis: 0.419

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.189

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spata19

Gene ontology

• Biological process: multicellular organism development;spermatogenesis;cell differentiation
• Cellular component: mitochondrial outer membrane