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Gene

SEMA3A

semaphorin 3A

Summary

Cytogenetic location
7q21.11
Coordinates
Chromosome 7: 83,955,777–84,194,789 (GRCh38)
Exons
17 exons across 239 kb
Protein
771 amino acids
Also known as
SEMA1, SemD, coll-1, Hsema-I
Previous symbols
SEMAD
MANE Select transcript
ENST00000265362.9NM_006080.3
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

  • Hypogonadotropic Hypogonadism

    • Abnormal ovarian or testicular function due to insufficient hormonal stimulation from the hypothalamic-pituitary axis.

      • 2 GenCC submitters rate it definitive or strong

How SEMA3A is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Stretches short reads find hard
Chromosome 7, with a bracket where SEMA3A sits. SEMA3A and 1 gene near it on chromosome 7, from 83,575,283 to 84,575,282.Chromosome 77q21.11p22.3p22.2p22.1p21.3p21.2p21.1p15.3p15.2p15.1p14.3p14.2p14.1p13p12.3p12.2p12.1p11.2p11.1q11.1q11.21q11.22q11.23q21.11q21.12q21.13q21.2q21.3q22.1q22.2q22.3q31.1q31.2q31.31q31.32q31.33q32.1q32.2q32.3q33q34q35q36.1q36.2q36.383.6 Mb83.8 Mb84 Mb84.2 Mb84.4 MbSEMA3E: 83,363,238–83,649,188, reverse strandSEMA3ESEMA3A: 83,955,777–84,194,789, reverse strandSEMA3ADiagram of SEMA3A: 17 exons on the reverse strand of chromosome 7Exon 17: 83,955,777–83,961,826, 6,050 basesExon 16: 83,963,205–83,963,347, 143 basesExon 15: 83,977,132–83,977,196, 65 basesExon 14: 83,981,321–83,981,478, 158 basesExon 13: 83,985,436–83,985,477, 42 basesExon 12: 84,001,955–84,002,046, 92 basesExon 11: 84,005,339–84,005,558, 220 basesExon 10: 84,007,353–84,007,497, 145 basesExon 9: 84,011,022–84,011,091, 70 basesExon 8: 84,011,183–84,011,297, 115 basesExon 7: 84,014,209–84,014,351, 143 basesExon 6: 84,046,324–84,046,443, 120 basesExon 5: 84,060,465–84,060,558, 94 basesExon 4: 84,110,470–84,110,589, 120 basesExon 3: 84,129,123–84,129,185, 63 basesExon 2: 84,134,794–84,134,951, 158 basesExon 1: 84,194,475–84,194,789, 315 bases171510515′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 8.1 kb of the gene's 239 kb; 2,316 of those bases code for the protein.

How a genome test reads SEMA3A

1

position in SEMA3A 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 239 kb of SEMA3A, introns included, not only the 8.1 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.). SEMA3A gene: semaphorin 3A. Retrieved 16 October 2026, from https://dantelabs.com/genes/sema3a

Vancouver

Dante Labs. SEMA3A gene: semaphorin 3A [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/sema3a

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