SSR2

signal sequence receptor subunit 2

Basic information

Region (hg38): 1:156009048-156020951

Links

ENSG00000163479 ∙ NCBI:6746 ∙ OMIM:600867 ∙ HGNC:11324 ∙ Uniprot:P43308 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 24.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_003145.4	NP_003136.1	5	yes	-
ENST00000295702.9	ENSP00000295702.4	5	yes	-
ENST00000480567.5	ENSP00000434306.1	5	-	-
ENST00000473699.5	ENSP00000432831.1	2	-	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SSR2 gene.

• not_specified (12 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SSR2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_003145.4. 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			1			1
missense			12			12
nonsense			2			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1			1
Total	0	0	16	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SSR2	protein_coding	protein_coding	ENST00000295702	5	11912

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125734	0	12	125746	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.945	77	104	0.739	0.00000573	1164
Missense in Polyphen		27	39.304	0.68695		429
Synonymous	1.07	35	44.0	0.795	0.00000244	388
Loss of Function	2.29	3	11.3	0.265	7.64e-7	103

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000704	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
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: 0.172

Intolerance Scores

• loftool: 0.283
• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.28

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.781

Gene Damage Prediction

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

Gene ontology

• Biological process: cotranslational protein targeting to membrane
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane
• Molecular function: protein binding