SRMS

src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristylation sites, the group of SH2 domain containing|PTK6 family tyrosine kinases

Basic information

Region (hg38): 20:63538489-63547749

Previous symbols: [ "C20orf148" ]

Links

ENSG00000125508 ∙ NCBI:6725 ∙ OMIM:617797 ∙ HGNC:11298 ∙ Uniprot:Q9H3Y6 ∙ 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 SRMS gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SRMS 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	2
missense			51	6		57
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	51	7	1

Variants in SRMS

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

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

Position	Type	Phenotype	Significance	ClinVar
20-63540830-T-G		not specified	Uncertain significance (Nov 12, 2024)
20-63540855-C-T		not specified	Likely benign (Aug 20, 2024)
20-63540874-G-T		not specified	Uncertain significance (Sep 15, 2021)
20-63540927-G-A		not specified	Uncertain significance (Dec 12, 2022)
20-63540942-G-A		not specified	Uncertain significance (Oct 03, 2022)
20-63540943-G-C		not specified	Uncertain significance (Jun 07, 2024)
20-63540945-C-T		not specified	Uncertain significance (Jan 19, 2022)
20-63540955-G-A		not specified	Uncertain significance (Sep 29, 2023)
20-63540973-G-T		not specified	Uncertain significance (Sep 01, 2021)
20-63540981-G-A		not specified	Uncertain significance (Jan 23, 2025)
20-63541272-C-T		not specified	Likely benign (Oct 16, 2024)
20-63541281-T-C		not specified	Uncertain significance (Jan 31, 2024)
20-63541331-G-A		not specified	Uncertain significance (Jan 10, 2023)
20-63541334-G-A		not specified	Uncertain significance (Mar 04, 2024)
20-63541477-A-G		not specified	Uncertain significance (Nov 13, 2024)
20-63541486-C-T		not specified	Uncertain significance (Sep 01, 2021)
20-63541501-C-T		not specified	Uncertain significance (Feb 12, 2024)
20-63541521-C-T		not specified	Uncertain significance (Feb 22, 2024)
20-63541524-T-A		not specified	Uncertain significance (Jul 27, 2024)
20-63541531-C-T		not specified	Likely benign (Dec 28, 2022)
20-63541599-C-T		not specified	Uncertain significance (Feb 14, 2023)
20-63541600-G-A		not specified	Uncertain significance (Aug 04, 2023)
20-63541609-G-A		not specified	Uncertain significance (May 30, 2023)
20-63542188-C-G			Uncertain significance (Jun 19, 2020)
20-63542193-G-A		not specified	Uncertain significance (Feb 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SRMS	protein_coding	protein_coding	ENST00000217188	8	6695

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.27e-12	0.0255	125438	0	81	125519	0.000323

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.00752	307	307	0.999	0.0000218	3072
Missense in Polyphen		107	105.14	1.0176		1173
Synonymous	0.681	134	144	0.928	0.0000110	1022
Loss of Function	-0.112	18	17.5	1.03	8.06e-7	213

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000913	0.000890
Ashkenazi Jewish	0.00	0.00
East Asian	0.000765	0.000762
Finnish	0.000140	0.000139
European (Non-Finnish)	0.000168	0.000159
Middle Eastern	0.000765	0.000762
South Asian	0.00100	0.000915
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Non-receptor tyrosine-protein kinase which phosphorylates DOK1 on tyrosine residues (PubMed:23822091). Also phosphorylates KHDRBS1/SAM68 and VIM on tyrosine residues (PubMed:29496907). Phosphorylation of KHDRBS1 is EGF-dependent (PubMed:29496907). {ECO:0000269|PubMed:23822091, ECO:0000269|PubMed:29496907}.
• Pathway: Focal Adhesion;Signaling by PTK6;Signal Transduction;PTK6 Down-Regulation;Signaling by Non-Receptor Tyrosine Kinases (Consensus)

Recessive Scores

• pRec: 0.238

Intolerance Scores

• loftool: 0.344
• rvis_EVS: 0.99
• rvis_percentile_EVS: 90.48

Haploinsufficiency Scores

• pHI: 0.0534
• hipred: N
• hipred_score: 0.289
• ghis: 0.414

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.266

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Srms
• Phenotype: normal phenotype

Gene ontology

• Biological process: transmembrane receptor protein tyrosine kinase signaling pathway;negative regulation of signal transduction;peptidyl-tyrosine phosphorylation;cell differentiation;peptidyl-tyrosine autophosphorylation
• Cellular component: cytoplasm;cytosol;extrinsic component of cytoplasmic side of plasma membrane
• Molecular function: protein tyrosine kinase activity;non-membrane spanning protein tyrosine kinase activity;signaling receptor binding;protein binding;ATP binding