SPATA16

protein-coding

spermatogenesis associated 16

Gene summary

This gene encodes a testis-specific protein that belongs to the tetratricopeptide repeat-like superfamily. The encoded protein localizes to the Golgi apparatus and may play a role in spermatogenesis. [provided by RefSeq, May 2010]

MANE transcript

NM_031955.6

Inheritance

ClinVar variants

U:89B:12

Top phenotype

Spermatogenic failure 6

gnomAD constraint

pLI —, LoF o/e 0.72

Max pathogenic AF

—

Genomic locus

chr3:172,889,357-173,141,235

External References & Databases

Ensembl (ENSG00000144962)

Transcript & Mutation Effects

hg38 • Region Span ~251.9 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

spermatogenic failure 6LIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0007060

Submitter: Labcorp Genetics (formerly Invitae)

spermatogenic failure 6MODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0007060

Submitter: PanelApp Australia

male infertility due to globozoospermiaSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0015746

Submitter: Orphanet

Clinical Genomic Database (CGD)

Spermatogenic failure 6AR

Manifestation: Genitourinary

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 17847006

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SPATA16 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 67

Spermatogenic failure 6Total: 38

not providedTotal: 8

SPATA16-related disorderTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_031955.6. 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			10 clinvar	3 clinvar		13
missense			74 clinvar	8 clinvar	1 clinvar	83
nonsense			1 clinvar			1
start loss						0
frameshift			3 clinvar			3
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	89	11	1	101

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_031955.6	RefSeq	NP_114161.3	10	MANE Select
ENST00000351008.4	Ensembl	ENSP00000341765.3	10	MANE Select
ENST00000652082.1	Ensembl	ENSP00000498213.1	6	Standard
ENST00001130912.1	Ensembl	ENSP00000800717.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

multicellular organism development
spermatogenesis
biological_process
cell differentiation

Molecular Function

molecular_function

Cellular Component

Golgi apparatus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000351008
Coding exons: 10
Length: 251911
Individuals with no LoFs: 124719
Homozygous LoFs: 0
Heterozygous LoFs: 1028
Defined: 125747
p: 0.00410

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.201	285	295	0.967	0.0000150	3783
Missense (PolyPhen)		11	12.933	0.85055		152
Synonymous	0.159	94	96.0	0.979	0.00000471	1012
Loss of Function	1.31	19	26.2	0.724	0.00000121	345

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0077	0.0073	notable
Latino/Admixed American	0.0019	0.0019	notable
Ashkenazi Jewish	0.0020	0.0020	notable
East Asian	0.0075	0.0074	notable
Finnish	0.0028	0.0025	notable
European (Non-Finnish)	0.0050	0.0049	notable
South Asian	0.0018	0.0018	notable
Other	0.0030	0.0029	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in the formation of sperm acrosome, which implicated its potential role in spermatogenesis and sperm-egg fusion. {ECO:0000269|PubMed:12529416}.;

Intolerance Scores

LoFtool: 0.942
RVIS EVS: 1.73
RVIS percentile EVS: 96.6

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 9.58e-10

Gene Damage Prediction

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