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CALHM4 calcium homeostasis modulator family member 4 [ Homo sapiens (human) ]

Gene ID: 221301, updated on 11-Apr-2024

Summary

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Official Symbol
CALHM4provided by HGNC
Official Full Name
calcium homeostasis modulator family member 4provided by HGNC
Primary source
HGNC:HGNC:21094
See related
Ensembl:ENSG00000164451 AllianceGenome:HGNC:21094
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
FAM26D; C6orf78
Summary
Predicted to enable cation channel activity. Predicted to be involved in cation transmembrane transport. Predicted to be integral component of membrane. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Restricted expression toward placenta (RPKM 4.4) See more
Orthologs
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Genomic context

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See CALHM4 in Genome Data Viewer
Location:
6q22.1
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (116529043..116561127)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (117712775..117744838)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (116850206..116882290)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24992 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24993 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17495 Neighboring gene CALHM6 antisense RNA 1 Neighboring gene calcium homeostasis modulator family member 6 Neighboring gene trafficking protein particle complex subunit 3L Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr6:116832513-116833094 Neighboring gene calcium homeostasis modulator family member 5 Neighboring gene MPRA-validated peak6051 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24994 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24995 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17496 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24996 Neighboring gene RWD domain containing 1 Neighboring gene MPRA-validated peak6052 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24997 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24998 Neighboring gene uncharacterized LOC124901386 Neighboring gene radial spoke head component 4A

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. Cryo-EM structures and functional properties of CALHM channels of the human placenta. Drożdżyk K, et al. Elife, 2020 May 6. PMID 32374262, Free PMC Article
  2. The DNA sequence and analysis of human chromosome 6. Mungall AJ, et al. Nature, 2003 Oct 23. PMID 14574404
  3. Sequential genome-wide CRISPR-Cas9 screens identify genes regulating cell-surface expression of tetraspanins. Yang J, et al. Cell Rep, 2023 Feb 28. PMID 36724073
  4. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. Clark HF, et al. Genome Res, 2003 Oct. PMID 12975309, Free PMC Article
  5. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Kimura K, et al. Genome Res, 2006 Jan. PMID 16344560, Free PMC Article

See all (12) citations in PubMed

GeneRIFs: Gene References Into Functions

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Homology

Clone Names

  • FLJ32239

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables monoatomic cation channel activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in monoatomic cation transmembrane transport IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in membrane IEA
Inferred from Electronic Annotation
more info
  
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
calcium homeostasis modulator protein 4
Names
family with sequence similarity 26 member D
protein FAM26D

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.

mRNA and Protein(s)

  1. NM_001256887.3 → NP_001243816.1  calcium homeostasis modulator protein 4 isoform a

    See identical proteins and their annotated locations for NP_001243816.1

    Status: VALIDATED

    Source sequence(s)
    AK056801, AK300309, AL121953, BC057769
    Consensus CDS
    CCDS59032.1
    UniProtKB/Swiss-Prot
    Q5JW98
    Related
    ENSP00000385836.1, ENST00000405399.5
    Conserved Domains (1) summary
    pfam14798
    Location:8 → 114
    Ca_hom_mod; Calcium homeostasis modulator

  2. NM_001256888.3 → NP_001243817.1  calcium homeostasis modulator protein 4 isoform b

    See identical proteins and their annotated locations for NP_001243817.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and 5' coding region, and uses an alternate start codon, compared to variant 1. The encoded isoform (b) has a distinct and shorter N-terminus, compared to isoform a.
    Source sequence(s)
    AK056801, AK300309, AL121953
    Consensus CDS
    CCDS59031.1
    UniProtKB/Swiss-Prot
    Q5JW98
    Related
    ENSP00000487169.1, ENST00000628083.1
    Conserved Domains (1) summary
    pfam14798
    Location:14 → 113
    Ca_hom_mod; Calcium homeostasis modulator

  3. NM_001256889.3 → NP_001243818.1  calcium homeostasis modulator protein 4 isoform c

    See identical proteins and their annotated locations for NP_001243818.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region and uses a downstream in-frame start codon, compared to variant 1. The encoded isoform (c) is shorter at the N-terminus, compared to isoform a. Both variants 3 and 4 encode isoform c.
    Source sequence(s)
    AK056801, AK300309, AL121953, DA855717
    Consensus CDS
    CCDS5109.1
    UniProtKB/TrEMBL
    B0QZ26
    Related
    ENSP00000409556.1, ENST00000452373.5
    Conserved Domains (1) summary
    pfam14798
    Location:1 → 71
    Ca_hom_mod; Calcium homeostasis modulator

  4. NM_001366078.2 → NP_001353007.1  calcium homeostasis modulator protein 4 isoform 5

    Status: VALIDATED

    Source sequence(s)
    AL121953
    Consensus CDS
    CCDS93991.1
    UniProtKB/Swiss-Prot
    B0QZ25, B0QZ27, B4DTQ0, Q5JW98, Q96MK0
    Related
    ENSP00000357585.3, ENST00000368596.4
    Conserved Domains (1) summary
    pfam14798
    Location:8 → 257
    Ca_hom_mod; Calcium homeostasis modulator

  5. NM_153036.5 → NP_694581.1  calcium homeostasis modulator protein 4 isoform c

    See identical proteins and their annotated locations for NP_694581.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks a portion of the 5' coding region and uses a downstream in-frame start codon, compared to variant 1. The encoded isoform (c) is shorter at the N-terminus, compared to isoform a. Both variants 3 and 4 encode isoform c.
    Source sequence(s)
    AK056801, AL121953, AY358252
    Consensus CDS
    CCDS5109.1
    UniProtKB/TrEMBL
    B0QZ26
    Related
    ENSP00000357586.2, ENST00000368597.6
    Conserved Domains (1) summary
    pfam14798
    Location:1 → 71
    Ca_hom_mod; Calcium homeostasis modulator

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    116529043..116561127
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011535562.3 → XP_011533864.1  calcium homeostasis modulator protein 4 isoform X3

    See identical proteins and their annotated locations for XP_011533864.1

    Conserved Domains (1) summary
    pfam14798
    Location:25 → 128
    Ca_hom_mod; Calcium homeostasis modulator

  2. XM_011535560.3 → XP_011533862.1  calcium homeostasis modulator protein 4 isoform X3

    See identical proteins and their annotated locations for XP_011533862.1

    Conserved Domains (1) summary
    pfam14798
    Location:25 → 128
    Ca_hom_mod; Calcium homeostasis modulator

  3. XM_017010390.2 → XP_016865879.1  calcium homeostasis modulator protein 4 isoform X1

  4. XM_017010391.2 → XP_016865880.1  calcium homeostasis modulator protein 4 isoform X2

  5. XM_011535561.3 → XP_011533863.1  calcium homeostasis modulator protein 4 isoform X3

    See identical proteins and their annotated locations for XP_011533863.1

    Conserved Domains (1) summary
    pfam14798
    Location:25 → 128
    Ca_hom_mod; Calcium homeostasis modulator

  6. XM_017010392.2 → XP_016865881.1  calcium homeostasis modulator protein 4 isoform X3

    Conserved Domains (1) summary
    pfam14798
    Location:25 → 128
    Ca_hom_mod; Calcium homeostasis modulator

  7. XM_011535563.3 → XP_011533865.1  calcium homeostasis modulator protein 4 isoform X3

    See identical proteins and their annotated locations for XP_011533865.1

    Conserved Domains (1) summary
    pfam14798
    Location:25 → 128
    Ca_hom_mod; Calcium homeostasis modulator

  8. XM_011535564.2 → XP_011533866.1  calcium homeostasis modulator protein 4 isoform X3

    See identical proteins and their annotated locations for XP_011533866.1

    Conserved Domains (1) summary
    pfam14798
    Location:25 → 128
    Ca_hom_mod; Calcium homeostasis modulator

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    117712775..117744838
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054354525.1 → XP_054210500.1  calcium homeostasis modulator protein 4 isoform X3

  2. XM_054354523.1 → XP_054210498.1  calcium homeostasis modulator protein 4 isoform X3

  3. XM_054354521.1 → XP_054210496.1  calcium homeostasis modulator protein 4 isoform X1

  4. XM_054354522.1 → XP_054210497.1  calcium homeostasis modulator protein 4 isoform X2

  5. XM_054354524.1 → XP_054210499.1  calcium homeostasis modulator protein 4 isoform X3

  6. XM_054354527.1 → XP_054210502.1  calcium homeostasis modulator protein 4 isoform X3

  7. XM_054354526.1 → XP_054210501.1  calcium homeostasis modulator protein 4 isoform X3

  8. XM_054354528.1 → XP_054210503.1  calcium homeostasis modulator protein 4 isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5JW98.1 GenPept UniProtKB/Swiss-Prot:Q5JW98

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