SLAIN2

SLAIN motif family member 2

Basic information

Region (hg38): 4:48341529-48426201

Previous symbols: [ "KIAA1458" ]

Links

ENSG00000109171 ∙ NCBI:57606 ∙ OMIM:610492 ∙ HGNC:29282 ∙ Uniprot:Q9P270 ∙ 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 SLAIN2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLAIN2 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					1	1
missense			42	2		44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	42	2	1

Variants in SLAIN2

This is a list of pathogenic ClinVar variants found in the SLAIN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-48341746-G-A		not specified	Uncertain significance (Jul 16, 2024)
4-48341761-G-T		not specified	Uncertain significance (Feb 06, 2024)
4-48341768-C-T		not specified	Uncertain significance (May 30, 2023)
4-48341848-G-A		not specified	Uncertain significance (Mar 29, 2023)
4-48341851-G-A		not specified	Uncertain significance (Aug 05, 2023)
4-48341878-G-C		not specified	Uncertain significance (Feb 23, 2023)
4-48341885-C-G		not specified	Uncertain significance (Nov 15, 2023)
4-48341908-C-T		not specified	Uncertain significance (Aug 28, 2023)
4-48341912-C-T		not specified	Uncertain significance (Jun 04, 2024)
4-48341962-T-G		not specified	Uncertain significance (Dec 03, 2021)
4-48341963-C-T		not specified	Uncertain significance (Nov 15, 2024)
4-48341978-G-C		not specified	Uncertain significance (Aug 17, 2022)
4-48341980-T-G		not specified	Uncertain significance (Jul 13, 2021)
4-48342007-G-C		not specified	Uncertain significance (Jan 27, 2022)
4-48342020-C-G		not specified	Uncertain significance (Jun 10, 2024)
4-48342020-C-T		not specified	Uncertain significance (Sep 01, 2021)
4-48342049-G-T		not specified	Uncertain significance (May 23, 2023)
4-48342060-C-A		not specified	Uncertain significance (Dec 18, 2023)
4-48342061-G-C		not specified	Uncertain significance (Sep 16, 2021)
4-48342076-C-G		not specified	Uncertain significance (Dec 22, 2023)
4-48369883-A-T		not specified	Uncertain significance (Jun 18, 2024)
4-48369890-A-G		not specified	Uncertain significance (Sep 29, 2023)
4-48369893-C-T		not specified	Uncertain significance (Feb 16, 2023)
4-48369991-A-G		not specified	Uncertain significance (Nov 09, 2023)
4-48377896-C-T		not specified	Uncertain significance (Jan 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLAIN2	protein_coding	protein_coding	ENST00000264313	8	84891

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.793	0.207	124624	0	15	124639	0.0000602

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.720	258	293	0.882	0.0000159	3706
Missense in Polyphen		96	147.55	0.65064		1699
Synonymous	0.479	96	102	0.940	0.00000501	1202
Loss of Function	3.65	4	22.8	0.176	0.00000129	287

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000203	0.000203
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000556
Finnish	0.0000930	0.0000928
European (Non-Finnish)	0.0000448	0.0000442
Middle Eastern	0.0000556	0.0000556
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to the plus end of microtubules and regulates microtubule dynamics and microtubule organization. Promotes cytoplasmic microtubule nucleation and elongation. Required for normal structure of the microtubule cytoskeleton during interphase. {ECO:0000269|PubMed:21646404}.

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.308
• rvis_EVS: -0.29
• rvis_percentile_EVS: 32.94

Haploinsufficiency Scores

• pHI: 0.728
• hipred: Y
• hipred_score: 0.783
• ghis: 0.643

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.693

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slain2

Gene ontology

• Biological process: microtubule nucleation;positive regulation of microtubule polymerization;cytoplasmic microtubule organization
• Cellular component: centrosome;cytosol;microtubule cytoskeleton;microtubule plus-end
• Molecular function: protein binding