SCIMP

SLP adaptor and CSK interacting membrane protein

Basic information

Region (hg38): 17:5208920-5234860

Previous symbols: [ "C17orf87" ]

Links

ENSG00000161929 ∙ NCBI:388325 ∙ OMIM:614406 ∙ HGNC:33504 ∙ Uniprot:Q6UWF3 ∙ 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 SCIMP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCIMP 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			4	2		6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	2	0

Variants in SCIMP

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

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

Position	Type	Phenotype	Significance	ClinVar
17-5214937-G-C		not specified	Uncertain significance (Nov 08, 2022)
17-5214940-A-C		not specified	Uncertain significance (Apr 20, 2024)
17-5214981-G-A		not specified	Uncertain significance (Jan 29, 2024)
17-5214983-C-G		not specified	Uncertain significance (Aug 29, 2024)
17-5221317-T-C		not specified	Uncertain significance (Oct 13, 2023)
17-5223377-A-G		not specified	Uncertain significance (Dec 10, 2024)
17-5223379-A-G		Head and neck cancer	Uncertain significance (Jun 10, 2019)
17-5223392-A-G		not specified	Uncertain significance (Sep 26, 2023)
17-5223393-C-T		not specified	Likely benign (Jan 30, 2024)
17-5223402-C-T		not specified	Uncertain significance (Apr 20, 2024)
17-5234744-G-T		not specified	Likely benign (Jun 09, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCIMP	protein_coding	protein_coding	ENST00000574081	5	25900

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000427	0.665	124790	0	5	124795	0.0000200

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.462	66	77.4	0.852	0.00000392	947
Missense in Polyphen		19	21.684	0.87622		268
Synonymous	0.648	26	30.6	0.851	0.00000183	265
Loss of Function	0.754	6	8.35	0.719	4.56e-7	84

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.0000266	0.0000265
Middle Eastern	0.00	0.00
South Asian	0.0000375	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Lipid tetraspanin-associated transmembrane adapter/mediator involved in major histocompatibility complex (MHC) class II signaling transduction. Required in generating the calcium response and enhancing ERK activity upon MHC-II stimulation. {ECO:0000269|PubMed:21930792}.

Intolerance Scores

• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.25

Haploinsufficiency Scores

• pHI: 0.130
• hipred: N
• hipred_score: 0.146
• ghis: 0.612

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Scimp
• Phenotype: homeostasis/metabolism phenotype; growth/size/body region phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: positive regulation of ERK1 and ERK2 cascade
• Cellular component: immunological synapse;membrane;integral component of membrane;leading edge membrane;uropod membrane;tetraspanin-enriched microdomain
• Molecular function: protein binding