SLAIN1

protein-coding

SLAIN motif family member 1

Gene summary

Predicted to be involved in cytoplasmic microtubule organization; microtubule nucleation; and positive regulation of microtubule polymerization. Predicted to be located in microtubule plus-end. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C13orf32

MANE transcript

NM_001242868.2

Inheritance

—

ClinVar variants

U:52B:6

Top phenotype

SLAIN1-related disorder

gnomAD constraint

pLI —, LoF o/e 0.15

Max pathogenic AF

—

Genomic locus

chr13:77,697,687-77,764,242

External References & Databases

Ensembl (ENSG00000139737)

Transcript & Mutation Effects

hg38 • Region Span ~66.6 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 SLAIN1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 51

SLAIN1-related disorderTotal: 6

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001242868.2. 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				2 clinvar		2
missense			51 clinvar	4 clinvar		55
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	52	6	0	58

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 36 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001242868.2	RefSeq	NP_001229797.1	7	MANE Select
ENST00000418532.6	Ensembl	ENSP00000400921.2	7	MANE Select
NM_001040153.4	RefSeq	NP_001035243.2	7	Standard
NM_001242869.2	RefSeq	NP_001229798.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

Cellular Component

cytoplasm
cytoskeleton

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000488699
Coding exons: 7
Length: 66355
Individuals with no LoFs: 125738
Homozygous LoFs: 0
Heterozygous LoFs: 4
Defined: 125742
p: 0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.22	183	236	0.776	0.0000124	2751
Missense (PolyPhen)		24	33.225	0.72235		316
Synonymous	-0.410	96	91.0	1.05	0.00000488	867
Loss of Function	3.60	3	20.7	0.145	0.00000105	241

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	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)	0.000026	0.000026	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Microtubule plus-end tracking protein that might be involved in the regulation of cytoplasmic microtubule dynamics, microtubule organization and microtubule elongation. {ECO:0000269|PubMed:21646404}.;

Recessive Scores

pRec: 0.112

Intolerance Scores

LoFtool: 0.0492
RVIS EVS: -0.32
RVIS percentile EVS: 31.69

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.102

Gene Damage Prediction

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