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

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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.

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						0
missense			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	0	0

Variants in SERP1

This is a list of pathogenic ClinVar variants found in the SERP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-150544470-C-A		not specified	Uncertain significance (Jun 04, 2024)
3-150545769-G-C		not specified	Uncertain significance (Feb 27, 2024)
3-150546114-G-A		not specified	Uncertain significance (Mar 13, 2023)
3-150546806-G-A		not specified	Uncertain significance (Jan 22, 2024)
3-150546818-C-G		not specified	Uncertain significance (Nov 21, 2022)
3-150552359-G-A		not specified	Uncertain significance (May 05, 2023)
3-150558461-A-G		not specified	Uncertain significance (Jan 16, 2024)
3-150562603-G-A		not specified	Uncertain significance (Oct 29, 2021)
3-150563565-A-G		not specified	Uncertain significance (Oct 12, 2022)
3-150563596-A-G		not specified	Uncertain significance (Feb 05, 2024)
3-150564299-G-T		not specified	Uncertain significance (Apr 12, 2022)
3-150564312-T-G		not specified	Uncertain significance (May 25, 2022)
3-150564367-A-G		not specified	Uncertain significance (Dec 28, 2022)
3-150567762-A-C		not specified	Uncertain significance (Mar 29, 2022)
3-150568002-G-T		Dystonia 33	Uncertain significance (Sep 22, 2024)
3-150568006-C-A		not specified	Uncertain significance (Jun 04, 2024)
3-150568193-A-G		not specified	Uncertain significance (Mar 23, 2023)
3-150568213-C-A		not specified	Uncertain significance (Aug 26, 2022)
3-150571970-C-A		EIF2A-related disorder	Likely benign (Mar 10, 2023)
3-150572021-A-G		not specified	Uncertain significance (Jan 05, 2022)
3-150572054-A-G		not specified	Uncertain significance (Jan 16, 2024)
3-150572075-T-C		not specified	Uncertain significance (Oct 14, 2021)
3-150572093-C-G		not specified	Uncertain significance (Feb 21, 2024)
3-150572129-T-C		not specified	Uncertain significance (Dec 15, 2022)
3-150572246-C-T		not specified	Uncertain significance (May 05, 2023)

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
0.265	0.645	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

Haploinsufficiency Scores

• pHI: 0.226
• hipred: Y
• hipred_score: 0.501
• ghis: 0.565

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

Mouse Genome Informatics

• Gene name: Serp1
• Phenotype: skeleton phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); 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); homeostasis/metabolism phenotype; muscle phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype

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