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

    Gene ID: 221301, updated on 2-Nov-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 monoatomic cation channel activity. Predicted to be involved in ATP export and monoatomic cation transmembrane transport. Predicted to be located in membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Restricted expression toward placenta (RPKM 4.4) See more
    Orthologs
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (116529043..116561127)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (117712775..117744838)
    RS_2024_09 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 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. Structural features of heteromeric channels composed of CALHM2 and CALHM4 paralogs. Drożdżyk K, et al. Elife, 2024 Jun 18. PMID 38896440, Free PMC Article
    3. The DNA sequence and analysis of human chromosome 6. Mungall AJ, et al. Nature, 2003 Oct 23. PMID 14574404
    4. 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
    5. 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

    See all (13) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Structural features of heteromeric channels composed of CALHM2 and CALHM4 paralogs.
      Title: Structural features of heteromeric channels composed of CALHM2 and CALHM4 paralogs.
    Submit: New GeneRIF Correction

    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 ATP export IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in monoatomic cation transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    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_2024_08

    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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