SPIN3

protein-coding

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

Gene summary

Enables histone H3K4me3 reader activity. Predicted to be involved in regulation of DNA-templated transcription. Predicted to be active in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001010862.3

Inheritance

—

ClinVar variants

U:50B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chrX:56,818,298-56,995,827

External References & Databases

Ensembl (ENSG00000204271)

Transcript & Mutation Effects

hg38 • Region Span ~177.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SPIN3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 25

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001010862.3. 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			6 clinvar			6
missense			41 clinvar	1 clinvar		42
nonsense			3 clinvar			3
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	50	1	0	51

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 56 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001010862.3	RefSeq	NP_001010862.2	1	MANE Select
ENST00000374919.6	Ensembl	ENSP00000364054.3	1	MANE Select
ENST00000475785.7	Ensembl	ENSP00000436805.1	2	Standard
ENST00000478405.1	Ensembl	ENSP00000433337.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

gamete generation

Molecular Function

protein binding
methylated histone binding

Cellular Component

nucleoplasm
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000374919
Coding exons: 1
Length: 19168
Individuals with no LoFs: 125302
Homozygous LoFs: 2
Heterozygous LoFs: 4
Defined: 125308
p: 0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.09	68	98.4	0.691	0.00000702	1695
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000079	0.000063	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000025	0.000018	rare
South Asian	0.00011	0.000065	rare
Other	0.00022	0.00016	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.307

Gene Damage Prediction

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