SPIN3

spindlin family member 3, the group of Tudor domain containing|Spindlin family

Basic information

Region (hg38): X:56818298-56995827

Links

ENSG00000204271 ∙ NCBI:169981 ∙ ∙ HGNC:27272 ∙ Uniprot:Q5JUX0 ∙ 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 SPIN3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPIN3 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			11	1		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	1	0

Variants in SPIN3

This is a list of pathogenic ClinVar variants found in the SPIN3 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-56994223-T-C		not specified	Uncertain significance (Sep 26, 2023)
X-56994254-C-A		not specified	Uncertain significance (Aug 05, 2024)
X-56994325-C-T		not specified	Uncertain significance (Sep 27, 2022)
X-56994388-C-T		not specified	Uncertain significance (Nov 21, 2023)
X-56994576-C-G		not specified	Uncertain significance (Dec 14, 2022)
X-56994588-A-C		not specified	Uncertain significance (May 14, 2024)
X-56994641-T-C		not specified	Uncertain significance (Jul 10, 2024)
X-56994653-G-C		not specified	Uncertain significance (Feb 27, 2024)
X-56994734-C-T		not specified	Uncertain significance (Dec 28, 2023)
X-56994751-G-A		not specified	Uncertain significance (Oct 24, 2024)
X-56994811-C-T			Likely benign (Dec 01, 2022)
X-56994812-G-A		not specified	Uncertain significance (Oct 26, 2022)
X-56994823-G-A		not specified	Uncertain significance (Nov 12, 2024)
X-56994851-C-T		not specified	Uncertain significance (Mar 01, 2024)
X-56994868-A-C		not specified	Uncertain significance (Jun 18, 2024)
X-56994916-C-T		not specified	Uncertain significance (Aug 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPIN3	protein_coding	protein_coding	ENST00000374919	1	19168

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.778	0.215	125302	2	4	125308	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.09	68	98.4	0.691	0.00000702	1695
Missense in Polyphen		18	34.898	0.51579		665
Synonymous	0.570	34	38.5	0.883	0.00000300	505
Loss of Function	2.07	0	4.99	0.00	3.58e-7	96

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000785	0.0000632
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000245	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.000105	0.0000653
Other	0.000224	0.000164

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Exhibits H3K4me3-binding activity. {ECO:0000269|PubMed:29061846}.

Recessive Scores

• pRec: 0.134

Intolerance Scores

• loftool: 0.185
• rvis_EVS: -0.14
• rvis_percentile_EVS: 42.88

Haploinsufficiency Scores

• pHI: 0.191
• hipred: N
• hipred_score: 0.260
• ghis: 0.633

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Gene ontology

• Biological process: gamete generation
• Cellular component: nucleoplasm;cytosol
• Molecular function: protein binding;methylated histone binding