GeneBe

TSPYL1

protein-coding

TSPY like 1

Gene summary

The protein encoded by this gene is found in the nucleolus and is similar to that of a family of genes on the Y-chromosome. This gene is intronless. Defects in this gene are a cause of sudden infant death with dysgenesis of the testes syndrome (SIDDT). [provided by RefSeq, Dec 2009]

Previous symbols:
  • TSPYL

MANE transcript

NM_003309.4

Inheritance

AR

ClinVar variants

P:5U:66B:23

Top phenotype

Sudden infant death with dysgenesis of the testes syndrome; 46, XY disorder of sex development

gnomAD constraint

pLI —, LoF o/e 0.8

Max pathogenic AF

—

Genomic locus

chr6:116,267,760-116,279,930

External References & Databases

Ensembl (ENSG00000189241)NCBI Gene (7259)OMIM (604714)HGNC:12382GenCCUniProt (Q9H0U9)AlphaFoldClinVar (TSPYL1)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~12.2 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

sudden infant death-dysgenesis of the testes syndromeSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0012124

Submitter: Orphanet

sudden infant death-dysgenesis of the testes syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0012124

Submitter: Labcorp Genetics (formerly Invitae)

sudden infant death-dysgenesis of the testes syndromeMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0012124

Submitter: Ambry Genetics

sudden infant death-dysgenesis of the testes syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0012124

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Sudden infant death with dysgenesis of the testes syndrome; 46, XY disorder of sex developmentAR

Manifestation: Genitourinary; Neurologic

Intervention: General

Rationale: In Sudden infant death with dysgenesis of the testes syndrome, death has been described during inpatient cardiorespiratory monitoring; In 46, XY disorder of sexual development, individuals may have the potential for gonadal tumors; 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: 15273283; 19463995Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TSPYL1 variants in ClinVar

6 Conditions Cataloged
Inborn genetic diseasesTotal: 59
not providedTotal: 30
Sudden infant death-dysgenesis of the testes syndromeTotal: 10
TSPYL1-related disorderTotal: 6
not specifiedTotal: 4
DSE-related disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003309.4. 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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
14
clinvar
1
clinvar
 16
missense
63
clinvar
6
clinvar
2
clinvar
 71
nonsense
2
clinvar
1
clinvar
 3
start loss
0
frameshift
1
clinvar
2
clinvar
1
clinvar
 4
splice donor/acceptor (+/-2bp)
0
Total146620394

Highest pathogenic variant AF is 0.000032836124

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_003309.4RefSeqNP_003300.11MANE Select
ENST00000368608.4EnsemblENSP00000357597.41MANE Select
ENST00000652202.1EnsemblENSP00000498597.11Standard
ENST00001026776.1EnsemblENSP00000696593.11Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways

Biological Process

  • nucleosome assembly
  • biological_process

Molecular Function

  • enzyme binding

Cellular Component

  • nucleus
  • nucleolus

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000368608
Coding exons
1
Length
3326
Individuals with no LoFs
0
Homozygous LoFs
0
Heterozygous LoFs
0
Defined
0
p
0.00
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.4252302490.9240.00001332824
Missense (PolyPhen)3058.1950.51551726
Synonymous-3.3414097.91.430.00000511891
Loss of Function0.6941113.80.7987.62e-7156

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)00.0absent
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec
0.0960

Intolerance Scores

LoFtool
0.476
RVIS EVS
0.78
RVIS percentile EVS
87.14

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.779

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumHigh
CancerMediumMediumMedium
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