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

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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.

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				5	3	8
missense			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1		1	2
non coding			1	4	1	6
Total	0	0	13	9	4

Variants in SSR3

This is a list of pathogenic ClinVar variants found in the SSR3 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-156543230-G-A			Likely benign (Jun 14, 2024)
3-156543249-C-T			Uncertain significance (Dec 07, 2024)
3-156543253-T-C		not specified	Uncertain significance (Oct 03, 2023)
3-156543286-G-A			Likely benign (Jul 19, 2023)
3-156544317-T-C			Uncertain significance (Mar 25, 2024)
3-156544339-A-G		not specified	Uncertain significance (Nov 30, 2021)
3-156544357-C-T			Uncertain significance (Jun 24, 2024)
3-156544358-G-A			Likely benign (Jan 15, 2023)
3-156544390-A-C		not specified	Uncertain significance (Dec 06, 2022)
3-156544396-T-C			Uncertain significance (Oct 19, 2024)
3-156544412-A-T			Likely benign (Mar 01, 2023)
3-156544421-A-G			Benign (Dec 16, 2024)
3-156544443-C-G			Benign (Feb 03, 2025)
3-156544453-A-G			Likely benign (Nov 22, 2022)
3-156548853-C-T			Benign (Feb 03, 2025)
3-156548896-G-A			Uncertain significance (Oct 13, 2023)
3-156548916-C-G			Uncertain significance (Sep 12, 2023)
3-156548935-C-T			Uncertain significance (Dec 07, 2023)
3-156548976-A-G			Benign (Jan 23, 2025)
3-156548982-ATCCT-A		Congenital disorder of glycosylation	Likely pathogenic (-)
3-156548985-C-T			Benign (Feb 02, 2025)
3-156553646-C-T			Likely benign (Nov 02, 2023)
3-156553647-ATACT-A			Uncertain significance (Nov 29, 2023)
3-156553675-C-T			Likely benign (Mar 12, 2022)
3-156553699-C-T			Likely benign (Sep 07, 2022)

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
0.747	0.251	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

Haploinsufficiency Scores

• pHI: 0.170
• hipred: Y
• hipred_score: 0.754
• ghis: 0.628

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

Mouse Genome Informatics

• Gene name: Ssr3
• 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); embryo phenotype; respiratory system phenotype; cellular phenotype; growth/size/body region phenotype

Gene ontology

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