SNRK

SNF related kinase

Basic information

Region (hg38): 3:43286511-43424764

Links

ENSG00000163788 ∙ NCBI:54861 ∙ OMIM:612760 ∙ HGNC:30598 ∙ Uniprot:Q9NRH2 ∙ 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 SNRK gene.

• Inborn genetic diseases (19 variants)
• not provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNRK 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					6	6
missense			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	6

Variants in SNRK

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

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

Position	Type	Phenotype	Significance	ClinVar
3-43303224-G-T			Benign (Dec 31, 2019)
3-43303248-A-G			Benign (Dec 31, 2019)
3-43303259-A-G		not specified	Uncertain significance (Jan 03, 2024)
3-43303514-T-C		not specified	Uncertain significance (May 16, 2023)
3-43303615-A-C			Benign (Dec 31, 2019)
3-43340293-C-T			Benign (Dec 31, 2019)
3-43340310-G-A		not specified	Uncertain significance (Jan 23, 2023)
3-43340483-C-G		not specified	Uncertain significance (Jun 30, 2022)
3-43347529-C-T		not specified	Uncertain significance (Aug 04, 2023)
3-43347658-T-G		not specified	Uncertain significance (Dec 02, 2022)
3-43347659-T-G		not specified	Uncertain significance (Dec 02, 2022)
3-43347747-C-T			Benign (Dec 31, 2019)
3-43347827-A-C		not specified	Uncertain significance (Nov 22, 2023)
3-43347832-C-T		not specified	Uncertain significance (Nov 15, 2021)
3-43347916-C-T		not specified	Uncertain significance (Sep 30, 2022)
3-43348004-G-A			Uncertain significance (Oct 04, 2021)
3-43348017-A-G			Benign (Dec 31, 2019)
3-43348090-G-A		not specified	Uncertain significance (Jul 06, 2021)
3-43348130-G-A		not specified	Uncertain significance (Jan 26, 2023)
3-43348132-C-T		not specified	Uncertain significance (Sep 06, 2022)
3-43348156-A-G		not specified	Uncertain significance (Mar 07, 2023)
3-43348183-G-A		not specified	Uncertain significance (Jun 24, 2022)
3-43348207-A-G		not specified	Uncertain significance (May 26, 2022)
3-43348222-G-A		not specified	Uncertain significance (Jan 18, 2022)
3-43348225-T-G		not specified	Uncertain significance (Jan 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNRK	protein_coding	protein_coding	ENST00000296088	5	138253

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000386	124785	0	4	124789	0.0000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.47	242	449	0.539	0.0000255	5059
Missense in Polyphen		61	166.61	0.36613		1829
Synonymous	-0.731	184	172	1.07	0.00000995	1511
Loss of Function	4.40	0	22.6	0.00	0.00000116	297

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000466	0.0000464
European (Non-Finnish)	0.0000178	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in hematopoietic cell proliferation or differentiation. Potential mediator of neuronal apoptosis. {ECO:0000250|UniProtKB:Q63553, ECO:0000269|PubMed:12234663, ECO:0000269|PubMed:15733851}.

Recessive Scores

• pRec: 0.131

Intolerance Scores

• loftool: 0.0267
• rvis_EVS: -0.64
• rvis_percentile_EVS: 16.53

Haploinsufficiency Scores

• pHI: 0.255
• hipred: Y
• hipred_score: 0.728
• ghis: 0.592

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.986

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Snrk
• Phenotype: homeostasis/metabolism phenotype; muscle phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: snrkb
• Affected structure: angioblastic mesenchymal cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: protein phosphorylation;myeloid cell differentiation;intracellular signal transduction
• Cellular component: nucleus;cytoplasm
• Molecular function: magnesium ion binding;protein serine/threonine kinase activity;ATP binding