SSR4 (signal sequence receptor subunit 4)

Gene

• Entrez ID: 6748
• Gene name: Signal sequence receptor subunit 4
• Gene symbol: SSR4
• Synonyms (NCBI Gene): CDG1Y, TRAPD
• Chromosome: X
• Chromosome location: Xq28
• Summary: This gene encodes the delta subunit of the translocon-associated protein complex which is involved in translocating proteins across the endoplasmic reticulum membrane. The encoded protein is located in the Xq28 region and is arranged in a compact head-to-

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs606231298	T>-	Pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant
rs794729223	AG>-	Pathogenic-likely-pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant
rs1057518735	G>A	Pathogenic	Splice donor variant
rs1057518736	G>A	Pathogenic	Splice acceptor variant
rs1557072752	TAGACTCAGGAAATCACTCAGCCCTTTTGATCATCCCGCCCCTGCTCACAGTCAACAGGGTTCCTATGCGTCCAGTTAGGCCCGGCCATGGGGATCTGGCCTTGTGCCCCCGTAGGGAAGACCAATGCAGAGGGCCAGTCACGGGATTGGTGAGTGTTACTTGGTACCTCCTGCCAGGGACACTGCAGCCCCCAACTGGGCCTAGCCTGCCCACCTGCAGGCCGTGTGAGCAGCGCACAGGGCTCCTCTGCCCAC	Pathogenic	Intron variant, non coding transcript variant, splice acceptor variant, initiator codon variant, coding sequence variant, 5 prime UTR variant, splice donor variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT043411	hsa-miR-331-3p	CLASH	23622248
MIRT1392762	hsa-miR-1207-5p	CLIP-seq
MIRT1392763	hsa-miR-1252	CLIP-seq
MIRT1392764	hsa-miR-342-5p	CLIP-seq
MIRT1392765	hsa-miR-4436b-3p	CLIP-seq
MIRT1392766	hsa-miR-4446-3p	CLIP-seq
MIRT1392767	hsa-miR-4492	CLIP-seq
MIRT1392768	hsa-miR-4498	CLIP-seq
MIRT1392769	hsa-miR-4505	CLIP-seq
MIRT1392770	hsa-miR-4651	CLIP-seq
MIRT1392771	hsa-miR-4664-5p	CLIP-seq
MIRT1392772	hsa-miR-4731-5p	CLIP-seq
MIRT1392773	hsa-miR-4763-3p	CLIP-seq
MIRT1392774	hsa-miR-608	CLIP-seq
MIRT1392775	hsa-miR-762	CLIP-seq
MIRT1392763	hsa-miR-1252	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005783	Component	Endoplasmic reticulum	IDA
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005784	Component	Sec61 translocon complex	NAS	7492314, 9286695
GO:0005789	Component	Endoplasmic reticulum membrane	IEA
GO:0012505	Component	Endomembrane system	IBA
GO:0016020	Component	Membrane	IEA
GO:0070062	Component	Extracellular exosome	HDA	20458337

Other IDs

• MIM: 300090
• HGNC: 11326
• e!Ensembl: ENSG00000180879

Protein

• UniProt ID: P51571
• Protein name: Translocon-associated protein subunit delta (TRAP-delta) (Signal sequence receptor subunit delta) (SSR-delta)
• Protein 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.
• PDB: 8B6L
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF05404	TRAP-delta	11 → 172	Translocon-associated protein, delta subunit precursor (TRAP-delta)	Family

• Sequence:

  MAAMASLGALALLLLSSLSRCSAEACLEPQITPSYYTTSDAVISTETVFIVEISLTCKNR
  VQNMALYADVGGKQFPVTRGQDVGRYQVSWSLDHKSAHAGTYEVRFFDEESYSLLRKAQR
  NNEDISIIPPLFTVSVDHRGTWNGPWVSTEVLAAAIGLVIYYLAFSAKSHIQA

• Sequence length: 173

Pathways

KEGG:

Protein processing in endoplasmic reticulum

Associated diseases

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Nonpapillary renal cell carcinoma	Likely pathogenic	rs880003306	RCV005920739
SSR4-congenital disorder of glycosylation	Pathogenic; Likely pathogenic	rs2148450759, rs880003306, rs2148450972, rs606231298, rs2520529293, rs2520526295, rs1557072752, rs794729223, rs1057518736, rs2092142348, rs2092148846	RCV001788519 RCV001754538 RCV001807878 RCV000191048 RCV003147893 RCV003314515 RCV000412580 RCV000412666 RCV000412598 RCV001254133 RCV001264383
Thyroid cancer, nonmedullary, 1	Pathogenic	rs868996072	RCV005924366

Unknown
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
-	no classification for the single variant	rs2522319131	-
Ovarian serous cystadenocarcinoma	Uncertain significance	rs2520495803	RCV005928845
SSR4-related disorder	Uncertain significance; Likely benign; Benign	rs2520494311, rs2520538783, rs2520535071, rs11538940, rs782061175	RCV003399876 RCV003402114 RCV003901839 RCV003971410 RCV003902993

Associations from Text Mining
Disease Name	Relationship Type	References
Adenocarcinoma of Lung	Associate	35571564
Alzheimer Disease	Associate	35766008
Congenital Disorders of Glycosylation	Associate	24218363, 26264460
Esophageal Squamous Cell Carcinoma	Associate	39840762
Periodontitis	Associate	29921943