SARAF

store-operated calcium entry associated regulatory factor

Basic information

Region (hg38): 8:30063002-30083208

Previous symbols: [ "TMEM66" ]

Links

ENSG00000133872 ∙ NCBI:51669 ∙ OMIM:614768 ∙ HGNC:28789 ∙ Uniprot:Q96BY9 ∙ 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 SARAF gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SARAF 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			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	20	1	0

Variants in SARAF

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

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

Position	Type	Phenotype	Significance	ClinVar
8-30066029-G-A		not specified	Uncertain significance (Apr 13, 2022)
8-30066101-G-A		not specified	Uncertain significance (Dec 20, 2023)
8-30066867-G-A		not specified	Uncertain significance (Apr 24, 2023)
8-30066895-C-T		not specified	Uncertain significance (Aug 08, 2022)
8-30069729-A-C		not specified	Uncertain significance (Dec 15, 2022)
8-30069734-G-A		not specified	Uncertain significance (Feb 27, 2024)
8-30069753-C-T		not specified	Uncertain significance (Mar 22, 2023)
8-30069780-C-T		not specified	Uncertain significance (May 20, 2024)
8-30069804-C-T		not specified	Uncertain significance (Sep 25, 2023)
8-30069839-G-A		not specified	Uncertain significance (Dec 17, 2021)
8-30069842-G-A		not specified	Uncertain significance (Jan 19, 2024)
8-30069883-G-T		not specified	Uncertain significance (Aug 02, 2021)
8-30069885-G-A		not specified	Uncertain significance (Jun 17, 2024)
8-30069921-G-A		not specified	Uncertain significance (Sep 26, 2023)
8-30069990-C-T		not specified	Uncertain significance (May 10, 2024)
8-30073960-C-T		not specified	Uncertain significance (Jan 23, 2023)
8-30073964-T-G		not specified	Uncertain significance (Dec 01, 2023)
8-30073966-T-C		not specified	Uncertain significance (Aug 05, 2023)
8-30073971-T-C		not specified	Uncertain significance (Jan 04, 2022)
8-30073972-G-C		not specified	Uncertain significance (Oct 25, 2023)
8-30074007-C-T		not specified	Uncertain significance (Nov 10, 2022)
8-30074035-C-T		not specified	Likely benign (Apr 13, 2022)
8-30082867-G-A		not specified	Uncertain significance (Jan 09, 2024)
8-30082933-C-A		not specified	Uncertain significance (Dec 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SARAF	protein_coding	protein_coding	ENST00000256255	6	20196

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00199	0.979	124857	0	891	125748	0.00355

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.489	169	188	0.900	0.00000995	2142
Missense in Polyphen		73	81.748	0.89299		934
Synonymous	0.472	72	77.3	0.932	0.00000456	684
Loss of Function	2.06	7	15.8	0.442	6.66e-7	209

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00162	0.00158
Ashkenazi Jewish	0.00263	0.00218
East Asian	0.0000544	0.0000544
Finnish	0.0167	0.0139
European (Non-Finnish)	0.00393	0.00361
Middle Eastern	0.0000544	0.0000544
South Asian	0.00370	0.00311
Other	0.00515	0.00441

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Negative regulator of store-operated Ca(2+) entry (SOCE) involved in protecting cells from Ca(2+) overfilling. In response to cytosolic Ca(2+) elevation after endoplasmic reticulum Ca(2+) refilling, promotes a slow inactivation of STIM (STIM1 or STIM2)- dependent SOCE activity: possibly act by facilitating the deoligomerization of STIM to efficiently turn off ORAI when the endoplasmic reticulum lumen is filled with the appropriate Ca(2+) levels, and thus preventing the overload of the cell with excessive Ca(2+) ions. {ECO:0000269|PubMed:22464749}.

Recessive Scores

• pRec: 0.123

Intolerance Scores

• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.53

Haploinsufficiency Scores

• pHI: 0.222
• hipred: N
• hipred_score: 0.285
• ghis: 0.556

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Saraf

Gene ontology

• Biological process: calcium ion transport;regulation of store-operated calcium entry
• Cellular component: endoplasmic reticulum;integral component of endoplasmic reticulum membrane;endoplasmic reticulum-plasma membrane contact site
• Molecular function: protein binding