SLAIN1

SLAIN motif family member 1

Basic information

Region (hg38): 13:77697687-77764242

Previous symbols: [ "C13orf32" ]

Links

ENSG00000139737 ∙ NCBI:122060 ∙ OMIM:610491 ∙ HGNC:26387 ∙ Uniprot:Q8ND83 ∙ 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 SLAIN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLAIN1 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			27			27
nonsense						0
start loss						0
frameshift					2	2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	0	2

Variants in SLAIN1

This is a list of pathogenic ClinVar variants found in the SLAIN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-77697956-T-C		not specified	Uncertain significance (Oct 22, 2021)
13-77698034-A-G		not specified	Uncertain significance (Jan 19, 2024)
13-77698103-C-T		SLAIN1-related disorder	Likely benign (Apr 15, 2022)
13-77698132-T-TGG			Benign (Dec 08, 2017)
13-77698141-G-GC			Benign (Dec 08, 2017)
13-77698172-A-C		not specified	Uncertain significance (Sep 17, 2021)
13-77698365-A-G		not specified	Uncertain significance (Sep 14, 2021)
13-77698428-C-T		not specified	Uncertain significance (Jul 14, 2021)
13-77699039-G-A		SLAIN1-related disorder	Benign (Oct 07, 2019)
13-77719606-T-C		not specified	Uncertain significance (Jul 16, 2021)
13-77744340-G-A		not specified	Uncertain significance (Mar 02, 2023)
13-77744464-G-T		SLAIN1-related disorder	Benign (Sep 06, 2019)
13-77746562-G-T		not specified	Uncertain significance (Jan 08, 2024)
13-77746574-C-T		not specified	Uncertain significance (Jan 01, 2025)
13-77746675-C-T		not specified	Uncertain significance (Nov 28, 2023)
13-77746735-A-T		not specified	Uncertain significance (Aug 08, 2023)
13-77746738-C-T		not specified	Uncertain significance (Dec 14, 2024)
13-77746759-A-G		not specified	Uncertain significance (Apr 07, 2023)
13-77746817-C-T		not specified	Uncertain significance (Dec 22, 2023)
13-77746823-C-T		not specified	Uncertain significance (Aug 26, 2024)
13-77746832-A-G		not specified	Uncertain significance (Apr 23, 2024)
13-77753236-G-A		not specified	Uncertain significance (Apr 15, 2024)
13-77753285-C-T		SLAIN1-related disorder	Likely benign (Jun 12, 2019)
13-77753290-G-A		not specified	Uncertain significance (Feb 22, 2025)
13-77753292-A-G		not specified	Uncertain significance (May 31, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLAIN1	protein_coding	protein_coding	ENST00000488699	7	66355

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.901	0.0990	125738	0	4	125742	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.22	183	236	0.776	0.0000124	2751
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.434
• hipred: Y
• hipred_score: 0.604
• ghis: 0.556

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.102

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slain1

Gene ontology

• Cellular component: cytoplasm;cytoskeleton
• Molecular function: protein binding