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GeneBe

SERP1

stress associated endoplasmic reticulum protein 1

Basic information

Region (hg38): 3:150541997-150603228

Links

ENSG00000120742NCBI:27230OMIM:617674HGNC:10759Uniprot:Q9Y6X1AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

  • Inborn genetic diseases (2 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.

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
clinvar
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
3-150545769-G-C not specified Uncertain significance (Feb 27, 2024)2258094
3-150546114-G-A not specified Uncertain significance (Mar 13, 2023)2495525
3-150546806-G-A not specified Uncertain significance (Jan 22, 2024)3087850
3-150546818-C-G not specified Uncertain significance (Nov 21, 2022)2398814
3-150552359-G-A not specified Uncertain significance (May 05, 2023)2550582
3-150558461-A-G not specified Uncertain significance (Jan 16, 2024)3087847
3-150562603-G-A not specified Uncertain significance (Oct 29, 2021)2359648
3-150563565-A-G not specified Uncertain significance (Oct 12, 2022)2318434
3-150563596-A-G not specified Uncertain significance (Feb 05, 2024)3087848
3-150564299-G-T not specified Uncertain significance (Apr 12, 2022)2222099
3-150564312-T-G not specified Uncertain significance (May 25, 2022)3087849
3-150564367-A-G not specified Uncertain significance (Dec 28, 2022)2351017
3-150567762-A-C not specified Uncertain significance (Mar 29, 2022)2280621
3-150568193-A-G not specified Uncertain significance (Mar 23, 2023)2528891
3-150568213-C-A not specified Uncertain significance (Aug 26, 2022)2309134
3-150571970-C-A EIF2A-related condition Likely benign (Mar 10, 2023)3052231
3-150572021-A-G not specified Uncertain significance (Jan 05, 2022)2270207
3-150572054-A-G not specified Uncertain significance (Jan 16, 2024)3087851
3-150572075-T-C not specified Uncertain significance (Oct 14, 2021)3087852
3-150572093-C-G not specified Uncertain significance (Feb 21, 2024)3087853
3-150572129-T-C not specified Uncertain significance (Dec 15, 2022)2335692
3-150572246-C-T not specified Uncertain significance (May 05, 2023)2544753
3-150572291-G-A not specified Uncertain significance (Aug 30, 2022)2309750
3-150572342-A-C not specified Uncertain significance (Mar 06, 2023)2494318
3-150572375-A-C Marinesco-Sjögren syndrome Uncertain significance (Mar 14, 2024)3220936

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SERP1protein_codingprotein_codingENST00000479209 361235
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.2650.645125742021257440.00000795
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.9002237.50.5860.00000161429
Missense in Polyphen922.2550.4044260
Synonymous-0.5711613.31.206.09e-7113
Loss of Function1.2613.580.2791.52e-743

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00002890.0000289
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.00003400.0000327
Other0.000.00

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
essential_gene_gene_trap
gene_indispensability_pred
E
gene_indispensability_score
0.901

Gene Damage Prediction

AllRecessiveDominant
MendelianLowLowLow
Primary ImmunodeficiencyLowLowLow
CancerLowLowLow

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