SERP1

stress associated endoplasmic reticulum protein 1

Basic information

Region (hg38): 3:150541998-150603228

Links

ENSG00000120742 ∙ NCBI:27230 ∙ OMIM:617674 ∙ HGNC:10759 ∙ Uniprot:Q9Y6X1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 6.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_014445.4	NP_055260.1	3	yes	-
ENST00000239944.7	ENSP00000239944.2	3	yes	-
ENST00000479209.1	ENSP00000420076.1	3	-	-
ENST00000491660.1	ENSP00000419472.1	2	-	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SERP1 gene.

• not_specified (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SERP1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_014445.4. 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						0
missense			7			7
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1			1
Total	0	0	8	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SERP1	protein_coding	protein_coding	ENST00000479209	3	61235

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125742	0	2	125744	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.900	22	37.5	0.586	0.00000161	429
Missense in Polyphen		9	22.255	0.4044		260
Synonymous	-0.571	16	13.3	1.20	6.09e-7	113
Loss of Function	1.26	1	3.58	0.279	1.52e-7	43

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.0000340	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Interacts with target proteins during their translocation into the lumen of the endoplasmic reticulum. Protects unfolded target proteins against degradation during ER stress. May facilitate glycosylation of target proteins after termination of ER stress. May modulate the use of N-glycosylation sites on target proteins (By similarity). {ECO:0000250}.
• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;XBP1(S) activates chaperone genes;XBP1(S) activates chaperone genes;IRE1alpha activates chaperones;Unfolded Protein Response (UPR);Metabolism of proteins (Consensus)

Recessive Scores

• pRec: 0.163

Intolerance Scores

• loftool: 0.577
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.25

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.901

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Gene ontology

• Biological process: skeletal system development;glucose metabolic process;cellular protein modification process;protein glycosylation;plasma membrane organization;post-embryonic development;multicellular organism aging;protein transport;endoplasmic reticulum unfolded protein response;positive regulation of insulin secretion;IRE1-mediated unfolded protein response;positive regulation of translation;positive regulation of organ growth;muscle organ morphogenesis;positive regulation of growth hormone secretion
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;cytosol;ribosome;cytoplasmic microtubule;integral component of membrane
• Molecular function: protein binding