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

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Nonpapillary renal cell carcinoma	Likely pathogenic	rs880003306	RCV005920739	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
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	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Thyroid cancer, nonmedullary, 1	Pathogenic	rs868996072	RCV005924366	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
CONGENITAL DISORDER OF GLYCOSYLATION TYPE 1Y	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IY	—	CTD, HPO CTD, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SSR4-related disorder	Uncertain significance; Likely benign; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Absence of septum pellucidum	Absence Of Septum Pellucidum	HPO_DG			★☆☆☆☆ Found in Text Mining only
Alzheimer Disease	Alzheimer disease	Pubtator	35766008	Associate	★☆☆☆☆ Found in Text Mining only
Blood Coagulation Disorders	Blood Coagulation Disorders	HPO_DG			★☆☆☆☆ Found in Text Mining only
Clinodactyly	Clinodactyly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Clinodactyly of fingers	Clinodactyly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital disorder of glycosylation type 1y	Congenital Disorder Of Glycosylation	ORPHANET_DG	24218363		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital disorder of glycosylation type 1y	Congenital Disorder Of Glycosylation	CLINVAR_DG	24218363		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital disorder of glycosylation type 1y	Congenital Disorder Of Glycosylation	GENOMICS_ENGLAND_DG	24218363, 26264460		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital disorder of glycosylation type 1y	Congenital Disorder Of Glycosylation	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital Disorders of Glycosylation	Congenital disorder of glycosylation	Pubtator	24218363, 26264460	Associate	★☆☆☆☆ Found in Text Mining only
Congenital Disorders of Glycosylation	Congenital disorder of glycosylation	BEFREE	26264460		★☆☆☆☆ Found in Text Mining only
Esophageal Squamous Cell Carcinoma	Esophageal squamous cell carcinoma	Pubtator	39840762	Associate	★☆☆☆☆ Found in Text Mining only
Gastroesophageal reflux disease	Gastroesophageal Reflux Disease	HPO_DG			★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
Horseshoe Kidney	Horseshoe Kidney	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypoplasia of corpus callosum	Hypoplasia Of Corpus Callosum	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypospadias	Hypospadias	HPO_DG			★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Macrostomia	Macrostomia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Macrotia	Macrotia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Micrognathism	Micrognathism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Patent ductus arteriosus	Patent ductus arteriosus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Periodontitis	Periodontitis	Pubtator	29921943	Associate	★☆☆☆☆ Found in Text Mining only
Scoliosis, unspecified	Scoliosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
SSR4-CDG	Congenital Disorder Of Glycosylation	Orphanet			★☆☆☆☆ Found in Text Mining only
Strabismus	Strabismus	HPO_DG			★☆☆☆☆ Found in Text Mining only