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CRELD1 cysteine rich with EGF like domains 1 [ Homo sapiens (human) ]

Gene ID: 78987, updated on 2-Nov-2024

Summary

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Official Symbol
CRELD1provided by HGNC
Official Full Name
cysteine rich with EGF like domains 1provided by HGNC
Primary source
HGNC:HGNC:14630
See related
Ensembl:ENSG00000163703 MIM:607170; AllianceGenome:HGNC:14630
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
AVSD2; CIRRIN; JELANS
Summary
This gene encodes a member of a subfamily of epidermal growth factor-related proteins. The encoded protein is characterized by a cysteine-rich with epidermal growth factor-like domain. This protein may function as a cell adhesion molecule. Mutations in this gene are the cause of atrioventricular septal defect. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Apr 2010]
Expression
Ubiquitous expression in thyroid (RPKM 17.8), heart (RPKM 15.1) and 25 other tissues See more
Orthologs
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Genomic context

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See CRELD1 in Genome Data Viewer
Location:
3p25.3
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (9933834..9945406)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (9925824..9937392)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (9975518..9987090)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:9944736-9945405 Neighboring gene interleukin 17 receptor E Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14047 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14048 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14049 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:9958035-9958574 Neighboring gene RNA, U6 small nuclear 882, pseudogene Neighboring gene interleukin 17 receptor C Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:9970047-9970546 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14050 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14051 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19413 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:9980935-9981732 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:9987356-9988018 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:9988681-9989342 Neighboring gene 3p25 PRRT3 Alu-mediated recombination region Neighboring gene PRRT3 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14052 Neighboring gene proline rich transmembrane protein 3 Neighboring gene ER membrane protein complex subunit 3 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:10018113-10019312 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:10028343-10028990 Neighboring gene EMC3 antisense RNA 1 Neighboring gene FANCD2 pseudogene 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. CRELD1 variants are associated with bicuspid aortic valve in Turner syndrome. Pinnaro CT, et al. Hum Genet, 2023 Apr. PMID 36929416, Free PMC Article
  2. Detailed mapping of a congenital heart disease gene in chromosome 3p25. Green EK, et al. J Med Genet, 2000 Aug. PMID 10922384, Free PMC Article
  3. Analysis of CRELD1 as a candidate 3p25 atrioventicular septal defect locus (AVSD2). Zatyka M, et al. Clin Genet, 2005 Jun. PMID 15857420
  4. CRELD1 and GATA4 gene analysis in patients with nonsyndromic atrioventricular canal defects. Sarkozy A, et al. Am J Med Genet A, 2005 Dec 15. PMID 16278904
  5. CRELD1 mutations contribute to the occurrence of cardiac atrioventricular septal defects in Down syndrome. Maslen CL, et al. Am J Med Genet A, 2006 Nov 15. PMID 17036335

See all (46) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Biallelic CRELD1 variants cause a multisystem syndrome, including neurodevelopmental phenotypes, cardiac dysrhythmias, and frequent infections.
    Title: Biallelic CRELD1 variants cause a multisystem syndrome, including neurodevelopmental phenotypes, cardiac dysrhythmias, and frequent infections.
  2. CRELD1 variants are associated with bicuspid aortic valve in Turner syndrome.
    Title: CRELD1 variants are associated with bicuspid aortic valve in Turner syndrome.
  3. The CRELD1 gene is likely to have a major role in causation of AVSD phenotype in selected DS patients.
    Title: CRELD1 gene variants and atrioventricular septal defects in Down syndrome.
  4. Germline mutations in the NKX2-5, GATA4, and CRELD1 genes do not appear to be associated with CHD in Mexican DS patients.
    Title: Germline mutations in NKX2-5, GATA4, and CRELD1 are rare in a Mexican sample of Down syndrome patients with endocardial cushion and septal heart defects.
  5. Mutation of the CRELD1 gene increased the risk for atrioventricular septal defect.
    Title: [Potential role of CRELD1 gene in the pathogenesis of atrioventricular septal defect].
  6. we identified two CRELD1 haplotypes associated with AVSD phenotype among DS and euploid individuals.
    Title: Polymorphic haplotypes of CRELD1 differentially predispose Down syndrome and euploids individuals to atrioventricular septal defect.
  7. study indicates that deleterious CRELD1 missense mutations are specifically associated with AVSD and are not correlated with other aspects of the heterotaxy phenotype
    Title: Specific association of missense mutations in CRELD1 with cardiac atrioventricular septal defects in heterotaxy syndrome.
  8. SNP c.985 C>T of CRELD1 is involved in causing congenital heart disease in patients of Mysore, South India.
    Title: A maiden report on CRELD1 single-nucleotide polymorphism association in congenital heart disease patients of Mysore, South India.
  9. CRELD1 is likely to be an AVSD-susceptibility gene and CRELD1 mutations may increase the risk of developing a heart defect rather than being a direct causative mutation
    Title: Novel CRELD1 gene mutations in patients with atrioventricular septal defect.
  10. Observational study of gene-disease association. (HuGE Navigator)
    Title: Novel CRELD1 gene mutations in patients with atrioventricular septal defect.
Submit: New GeneRIF Correction See all GeneRIFs (13)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Atrioventricular septal defect, susceptibility to, 2
MedGen: C1853508 OMIM: 606217 GeneReviews: Not available
Compare labs
Jeffries-Lakhani neurodevelopmental syndrome
MedGen: CN377243 OMIM: 620771 GeneReviews: Not available
not available

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • DKFZp566D213

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables calcium ion binding IEA
Inferred from Electronic Annotation
more info
  
enables extracellular matrix structural constituent RCA
inferred from Reviewed Computational Analysis
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein disulfide isomerase activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in cardiac septum development TAS
Traceable Author Statement
more info
 PubMed 
involved_in endocardial cushion development TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in collagen-containing extracellular matrix HDA PubMed 
located_in glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
  
located_in membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
protein disulfide isomerase CRELD1
NP_001026887.2
NP_001070883.2
NP_001361245.1
NP_001361246.1
NP_001361247.1
NP_001361248.1
NP_001361249.1
NP_001397642.1
NP_056328.3
XP_011532410.1
XP_047304853.1
XP_047304854.1
XP_047304856.1
XP_054203808.1
XP_054203809.1
XP_054203810.1
XP_054203811.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_017069.2 RefSeqGene

    Range
    5002..16574
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001031717.4 → NP_001026887.2  protein disulfide isomerase CRELD1 isoform 1 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AC018809
    Consensus CDS
    CCDS33693.1
    UniProtKB/TrEMBL
    A0A804HJB9
    Related
    ENSP00000321856.5, ENST00000326434.9
    Conserved Domains (4) summary
    smart00179
    Location:305 → 336
    EGF_CA; Calcium-binding EGF-like domain
    smart00261
    Location:210 → 245
    FU; Furin-like repeats
    pfam11938
    Location:46 → 100
    DUF3456; TLR4 regulator and MIR-interacting MSAP
    cl21504
    Location:245 → 272
    EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...

  2. NM_001077415.3 → NP_001070883.2  protein disulfide isomerase CRELD1 isoform 2 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an exon in the 3' coding region, which results in a frameshift, compared to variant 1. The resulting protein (isoform 2) is shorter and has a distinct C-terminus, compared to isoform 1. Variants 2, 3, and 4 all encode the same isoform (2).
    Source sequence(s)
    AC018809
    Consensus CDS
    CCDS2593.1
    UniProtKB/Swiss-Prot
    A8MX90, B2RAA9, Q6I9X5, Q8NFT4, Q96HD1, Q9Y409
    UniProtKB/TrEMBL
    A0A804HKD9
    Related
    ENSP00000393643.2, ENST00000452070.6
    Conserved Domains (4) summary
    smart00179
    Location:305 → 336
    EGF_CA; Calcium-binding EGF-like domain
    smart00261
    Location:210 → 245
    FU; Furin-like repeats
    pfam11938
    Location:46 → 100
    DUF3456; TLR4 regulator and MIR-interacting MSAP
    cl21504
    Location:245 → 272
    EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...

  3. NM_001374316.1 → NP_001361245.1  protein disulfide isomerase CRELD1 isoform 2 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4), as well as variants 2 and 3, encodes isoform 2.
    Source sequence(s)
    AC018809
    Consensus CDS
    CCDS2593.1
    UniProtKB/Swiss-Prot
    A8MX90, B2RAA9, Q6I9X5, Q8NFT4, Q96HD1, Q9Y409
    UniProtKB/TrEMBL
    A0A804HKD9
    Related
    ENSP00000507127.1, ENST00000684493.1
    Conserved Domains (4) summary
    smart00179
    Location:305 → 336
    EGF_CA; Calcium-binding EGF-like domain
    smart00261
    Location:210 → 245
    FU; Furin-like repeats
    pfam11938
    Location:46 → 100
    DUF3456; TLR4 regulator and MIR-interacting MSAP
    cl21504
    Location:245 → 272
    EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...

  4. NM_001374317.1 → NP_001361246.1  protein disulfide isomerase CRELD1 isoform 3 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5), as well as variant 6, encodes isoform 3.
    Source sequence(s)
    AC018809
    Consensus CDS
    CCDS93207.1
    UniProtKB/TrEMBL
    A0A804HJB9, A0A804HJJ0
    Conserved Domains (4) summary
    smart00179
    Location:305 → 336
    EGF_CA; Calcium-binding EGF-like domain
    smart00261
    Location:210 → 245
    FU; Furin-like repeats
    pfam11938
    Location:46 → 100
    DUF3456; TLR4 regulator and MIR-interacting MSAP
    cl21504
    Location:245 → 272
    EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...

  5. NM_001374318.1 → NP_001361247.1  protein disulfide isomerase CRELD1 isoform 3 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6), as well as variant 5, encodes isoform 3.
    Source sequence(s)
    AC018809
    Consensus CDS
    CCDS93207.1
    UniProtKB/TrEMBL
    A0A804HJB9, A0A804HJJ0
    Related
    ENSP00000507522.1, ENST00000684181.1
    Conserved Domains (4) summary
    smart00179
    Location:305 → 336
    EGF_CA; Calcium-binding EGF-like domain
    smart00261
    Location:210 → 245
    FU; Furin-like repeats
    pfam11938
    Location:46 → 100
    DUF3456; TLR4 regulator and MIR-interacting MSAP
    cl21504
    Location:245 → 272
    EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...

  6. NM_001374319.1 → NP_001361248.1  protein disulfide isomerase CRELD1 isoform 4 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7), as well as variant 8, encodes isoform 4.
    Source sequence(s)
    AC018809
    Consensus CDS
    CCDS93208.1
    UniProtKB/TrEMBL
    A0A669KAV0, A0A804HKD9
    Related
    ENSP00000500961.2, ENST00000673935.2
    Conserved Domains (3) summary
    smart00179
    Location:277 → 308
    EGF_CA; Calcium-binding EGF-like domain
    smart00261
    Location:210 → 246
    FU; Furin-like repeats
    pfam11938
    Location:46 → 100
    DUF3456; TLR4 regulator and MIR-interacting MSAP

  7. NM_001374320.1 → NP_001361249.1  protein disulfide isomerase CRELD1 isoform 4 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8), as well as variant 7, encodes isoform 4.
    Source sequence(s)
    AC018809
    Consensus CDS
    CCDS93208.1
    UniProtKB/TrEMBL
    A0A669KAV0, A0A804HKD9
    Conserved Domains (3) summary
    smart00179
    Location:277 → 308
    EGF_CA; Calcium-binding EGF-like domain
    smart00261
    Location:210 → 246
    FU; Furin-like repeats
    pfam11938
    Location:46 → 100
    DUF3456; TLR4 regulator and MIR-interacting MSAP

  8. NM_001410713.1 → NP_001397642.1  protein disulfide isomerase CRELD1 isoform 5 precursor

    Status: REVIEWED

    Source sequence(s)
    AC018809
    Consensus CDS
    CCDS93206.1
    UniProtKB/TrEMBL
    A0A804HKP7
    Related
    ENSP00000508209.1, ENST00000682907.1

  9. NM_015513.6 → NP_056328.3  protein disulfide isomerase CRELD1 isoform 2 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and lacks an exon in the 3' coding region, which results in a frameshift, compared to variant 1. The resulting protein (isoform 2) is shorter and has a distinct C-terminus, compared to isoform 1. Variants 2, 3, and 4 all encode the same isoform (2).
    Source sequence(s)
    AC018809
    Consensus CDS
    CCDS2593.1
    UniProtKB/Swiss-Prot
    A8MX90, B2RAA9, Q6I9X5, Q8NFT4, Q96HD1, Q9Y409
    UniProtKB/TrEMBL
    A0A804HKD9
    Related
    ENSP00000373322.3, ENST00000383811.8
    Conserved Domains (4) summary
    smart00179
    Location:305 → 336
    EGF_CA; Calcium-binding EGF-like domain
    smart00261
    Location:210 → 245
    FU; Furin-like repeats
    pfam11938
    Location:46 → 100
    DUF3456; TLR4 regulator and MIR-interacting MSAP
    cl21504
    Location:245 → 272
    EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...

RNA

  1. NR_164475.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC018809
    Related
    ENST00000674067.2

  2. NR_164476.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC018809
    Related
    ENST00000682397.1

  3. NR_164477.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC018809

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    9933834..9945406
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011534108.2 → XP_011532410.1  protein disulfide isomerase CRELD1 isoform X2

    UniProtKB/TrEMBL
    A0A804HJB9, A0A804HJJ0
    Conserved Domains (4) summary
    smart00179
    Location:305 → 336
    EGF_CA; Calcium-binding EGF-like domain
    smart00261
    Location:210 → 245
    FU; Furin-like repeats
    pfam11938
    Location:46 → 100
    DUF3456; TLR4 regulator and MIR-interacting MSAP
    cl21504
    Location:245 → 272
    EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...

  2. XM_047448898.1 → XP_047304854.1  protein disulfide isomerase CRELD1 isoform X3

    Related
    ENSP00000507437.1, ENST00000683982.1

  3. XM_047448897.1 → XP_047304853.1  protein disulfide isomerase CRELD1 isoform X1

    UniProtKB/TrEMBL
    A0A804HKP7
    Related
    ENSP00000507251.1, ENST00000682642.1

  4. XM_047448900.1 → XP_047304856.1  protein disulfide isomerase CRELD1 isoform X4

    UniProtKB/TrEMBL
    A0A669KAV2, A0A669KBB3
    Related
    ENSP00000507258.1, ENST00000683547.1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    9925824..9937392
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054347834.1 → XP_054203809.1  protein disulfide isomerase CRELD1 isoform X2

  2. XM_054347835.1 → XP_054203810.1  protein disulfide isomerase CRELD1 isoform X3

  3. XM_054347833.1 → XP_054203808.1  protein disulfide isomerase CRELD1 isoform X1

  4. XM_054347836.1 → XP_054203811.1  protein disulfide isomerase CRELD1 isoform X4

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96HD1.3 GenPept UniProtKB/Swiss-Prot:Q96HD1

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