SRL

sarcalumenin

Basic information

Region (hg38): 16:4189374-4242080

Links

ENSG00000185739 ∙ NCBI:6345 ∙ OMIM:604992 ∙ HGNC:11295 ∙ Uniprot:Q86TD4 ∙ 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 SRL gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SRL 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					2	2
missense			33	1		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	1	2

Variants in SRL

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

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

Position	Type	Phenotype	Significance	ClinVar
16-4192190-C-T		not specified	Uncertain significance (Feb 14, 2023)
16-4192255-C-T			Benign (Dec 31, 2019)
16-4192296-A-G		not specified	Uncertain significance (Feb 02, 2024)
16-4192325-G-C		not specified	Uncertain significance (Apr 09, 2024)
16-4192329-G-A		not specified	Uncertain significance (Apr 27, 2024)
16-4192359-C-T		not specified	Uncertain significance (Apr 28, 2022)
16-4192376-G-A		not specified	Uncertain significance (Jun 25, 2024)
16-4192378-C-G		not specified	Uncertain significance (Jan 18, 2023)
16-4192467-C-T		not specified	Uncertain significance (Jan 24, 2025)
16-4192470-T-C		not specified	Uncertain significance (Jan 03, 2024)
16-4192476-C-G		not specified	Uncertain significance (Jan 02, 2025)
16-4192501-C-T		not specified	Uncertain significance (Jun 26, 2023)
16-4192535-A-G		not specified	Uncertain significance (Jan 10, 2023)
16-4192545-C-T		not specified	Uncertain significance (Feb 08, 2025)
16-4192553-C-T		not specified	Uncertain significance (Feb 12, 2025)
16-4192559-C-T		not specified	Uncertain significance (Dec 10, 2024)
16-4192579-G-T		not specified	Uncertain significance (Aug 15, 2023)
16-4192602-T-C		not specified	Uncertain significance (Apr 24, 2024)
16-4192713-C-T		not specified	Uncertain significance (Mar 01, 2025)
16-4192716-T-C		not specified	Uncertain significance (Mar 01, 2024)
16-4192853-C-T		not specified	Uncertain significance (Jun 06, 2023)
16-4192862-A-G		not specified	Uncertain significance (Feb 12, 2024)
16-4192893-T-C		not specified	Uncertain significance (Aug 02, 2021)
16-4192912-G-C		not specified	Uncertain significance (Jul 09, 2024)
16-4195562-G-C		not specified	Uncertain significance (Mar 11, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SRL	protein_coding	protein_coding	ENST00000399609	6	52707

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.00e-8	0.494	124764	0	37	124801	0.000148

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.473	263	285	0.921	0.0000177	3120
Missense in Polyphen		119	127.89	0.9305		1402
Synonymous	-2.16	145	115	1.26	0.00000708	923
Loss of Function	0.912	13	17.1	0.762	7.28e-7	212

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000646	0.0000645
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.000134	0.000132
Middle Eastern	0.000111	0.000111
South Asian	0.000491	0.000490
Other	0.000665	0.000660

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in the regulation of calcium transport.

Recessive Scores

• pRec: 0.210

Intolerance Scores

• loftool: 0.188
• rvis_EVS: -1.07
• rvis_percentile_EVS: 7.43

Haploinsufficiency Scores

• pHI: 0.276
• hipred: N
• hipred_score: 0.337
• ghis: 0.629

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0468

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Srl
• Phenotype: muscle phenotype; 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)

Gene ontology

• Cellular component: sarcoplasmic reticulum lumen
• Molecular function: GTP binding