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Gene

GPHN

gephyrin

Summary

Cytogenetic location
14q23.3
Coordinates
Chromosome 14: 66,508,147–67,181,803 (GRCh38)
Exons
23 exons across 673.7 kb
Protein
769 amino acids
Inheritance
Autosomal recessive
Also known as
KIAA1385, GEPH, GPH
MANE Select transcript
ENST00000478722.6NM_020806.5
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated report relevant to this gene

  • Molybdenum Cofactor & Isolated Sulfite Oxidase Deficiency

    • Molybdenum Cofactor DeficiencyAutosomal recessive

      A condition caused by changes in both copies of MOCS1, MOCS2 or GPHN, which are needed to make the molybdenum cofactor used by sulfite oxidase and other enzymes.

      • ClinGen rates the link moderate
      • 2 GenCC submitters rate it definitive or strong
      What knowing changes

      Fosdenopterin is an approved treatment for type A (MOCS1) and works best when started very early; carrier status is relevant to family planning.

Inheritance

Autosomal recessive
It takes a changed copy from each parent. With one, you are a carrier and usually unaffected; when both parents are carriers, each child has a one-in-four chance of inheriting two.

How GPHN is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 14, with a bracket where GPHN sits. GPHN and 16 genes near it on chromosome 14, from 65,834,490 to 67,855,460.Chromosome 1414q23.3p13p12p11.2p11.1q11.1q11.2q12q13.1q13.2q13.3q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.3q31.1q31.2q31.3q32.11q32.12q32.13q32.2q32.31q32.32q32.3366 Mb66.5 Mb67 Mb67.5 MbCCDC196: 66,411,704–66,498,677, forward strandCCDC196GPHN: 66,508,147–67,181,803, forward strandGPHNGARIN2: 67,189,328–67,228,550, forward strandGARIN2PALS1: 67,240,713–67,336,061, forward strandPALS1ATP6V1D: 67,294,371–67,360,265, reverse strandATP6V1DEIF2S1: 67,359,993–67,394,395, forward strandEIF2S1PLEK2: 67,385,652–67,412,236, reverse strandPLEK2TMEM229B: 67,447,084–67,533,878, reverse strandTMEM229BPLEKHH1: 67,533,063–67,589,725, forward strandPLEKHH1PIGH: 67,581,955–67,600,316, reverse strandPIGHARG2: 67,619,857–67,667,328, forward strandARG2VTI1B: 67,635,307–67,674,920, reverse strandVTI1B: 67,659,820–67,690,367, reverse strandRDH11: 67,676,792–67,695,793, reverse strandRDH12: 67,701,886–67,734,451, forward strandZFYVE26: 67,727,374–67,816,590, reverse strandZFYVE26RAD51B: 67,819,741–68,730,218, forward strandRAD51BDiagram of GPHN: 23 exons on the forward strand of chromosome 14Exon 3: 2 known disease-causing sitesExon 4: 1 known disease-causing siteExon 6: 1 known disease-causing siteExon 7: 4 known disease-causing sitesExon 8: 6 known disease-causing sitesExon 9: 1 known disease-causing siteExon 12: 5 known disease-causing sitesExon 13: 1 known disease-causing siteExon 15: 1 known disease-causing siteExon 16: 1 known disease-causing siteExon 17: 2 known disease-causing sitesExon 18: 1 known disease-causing siteExon 19: 1 known disease-causing siteExon 1: 66,508,147–66,508,591, 445 basesExon 2: 66,681,107–66,681,185, 79 basesExon 3: 66,776,464–66,776,521, 58 basesExon 4: 66,824,474–66,824,566, 93 basesExon 5: 66,879,939–66,880,033, 95 basesExon 6: 66,916,003–66,916,069, 67 basesExon 7: 66,922,666–66,922,938, 273 basesExon 8: 66,924,194–66,924,292, 99 basesExon 9: 66,965,191–66,965,325, 135 basesExon 10: 67,023,633–67,023,675, 43 basesExon 11: 67,058,649–67,058,786, 138 basesExon 12: 67,088,983–67,089,075, 93 basesExon 13: 67,100,856–67,100,911, 56 basesExon 14: 67,110,140–67,110,259, 120 basesExon 15: 67,111,861–67,111,919, 59 basesExon 16: 67,113,018–67,113,171, 154 basesExon 17: 67,122,256–67,122,377, 122 basesExon 18: 67,143,362–67,143,449, 88 basesExon 19: 67,159,415–67,159,488, 74 basesExon 20: 67,165,162–67,165,226, 65 basesExon 21: 67,168,933–67,169,036, 104 basesExon 22: 67,179,578–67,179,674, 97 basesExon 23: 67,180,804–67,181,803, 1,000 bases15101520235′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 3.6 kb of the gene's 673.7 kb; 2,310 of those bases code for the protein.

How a genome test reads GPHN

42

positions in GPHN where ClinVar classes a change as pathogenic or likely pathogenic

None of them falls in a region short reads find hard.

A whole genome covers all 673.7 kb of GPHN, introns included, not only the 3.6 kb of exons.

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). GPHN gene: gephyrin. Retrieved 17 October 2026, from https://dantelabs.com/genes/gphn

Vancouver

Dante Labs. GPHN gene: gephyrin [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/gphn

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