SSR3

signal sequence receptor subunit 3

Basic information

Region (hg38): 3:156539553-156555149

Links

ENSG00000114850 ∙ NCBI:6747 ∙ OMIM:606213 ∙ HGNC:11325 ∙ Uniprot:Q9UNL2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 13.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
ENST00000265044.7	ENSP00000265044.2	5	yes	-
ENST00000463503.5	ENSP00000417306.1	4	-	-
ENST00000467789.5	ENSP00000420641.1	5	-	-
ENST00000476217.5	ENSP00000417530.1	5	-	-

Phenotypes

GenCC

Source: genCC

• congenital disorder of glycosylation (Moderate), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SSR3 gene.

• not_provided (29 variants)
• not_specified (13 variants)
• Congenital_disorder_of_glycosylation (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SSR3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000007107.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				8	2	10
missense			24			24
nonsense						0
start loss						0
frameshift		1				1
splice donor/acceptor (+/-2bp)						0
Total	0	1	24	8	2

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SSR3	protein_coding	protein_coding	ENST00000265044	5	15045

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125117	0	1	125118	0.00000400

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.770	75	96.3	0.779	0.00000448	1208
Missense in Polyphen		10	27.418	0.36473		420
Synonymous	-1.01	45	37.2	1.21	0.00000178	353
Loss of Function	2.45	1	8.88	0.113	4.40e-7	111

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	0.00	0.00
European (Non-Finnish)	0.00000882	0.00000882
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: TRAP proteins are part of a complex whose function is to bind calcium to the ER membrane and thereby regulate the retention of ER resident proteins.
• Pathway: Protein processing in endoplasmic reticulum - Homo sapiens (human);SRP-dependent cotranslational protein targeting to membrane;Translation;Metabolism of proteins (Consensus)

Recessive Scores

• pRec: 0.130

Intolerance Scores

• loftool: 0.307
• rvis_EVS: -0.23
• rvis_percentile_EVS: 36.86

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.934

Gene Damage Prediction

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

Gene ontology

• Biological process: SRP-dependent cotranslational protein targeting to membrane
• Cellular component: endoplasmic reticulum membrane;integral component of membrane