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Gene

SETD1A

SET domain containing 1A, histone lysine methyltransferase

Summary

Cytogenetic location
16p11.2
Coordinates
Chromosome 16: 30,957,754–30,984,664 (GRCh38)
Exons
19 exons across 26.9 kb
Protein
1,707 amino acids
Also known as
KIAA0339, Set1, KMT2F, SET1A
MANE Select transcript
ENST00000262519.14NM_014712.3
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 reports relevant to this gene

No Genome Test report reads SETD1A yet. The test sequences your whole genome, so your data includes it all the same.

How SETD1A is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 16, with a bracket where SETD1A sits. SETD1A and 44 genes near it on chromosome 16, from 30,471,209 to 31,471,208.Chromosome 1616p11.2p13.3p13.2p13.13p13.12p13.11p12.3p12.2p12.1p11.2p11.1q11.1q11.2q12.1q12.2q13q21q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.330.6 Mb30.8 Mb31 Mb31.2 Mb31.4 MbITGAL: 30,472,658–30,523,567, forward strandZNF768: 30,524,001–30,527,328, reverse strand: 30,525,923–30,534,852, reverse strandZNF747: 30,529,534–30,535,347, reverse strandZNF747ZNF764: 30,553,764–30,558,524, reverse strandZNF764ZNF688: 30,569,281–30,572,734, reverse strandZNF688ZNF785: 30,573,740–30,585,806, reverse strandZNF785ZNF689: 30,602,558–30,624,012, reverse strandZNF689: 30,610,211–30,610,351, reverse strandPRR14: 30,650,696–30,656,427, forward strandPRR14FBRS: 30,658,431–30,670,810, forward strandFBRSSRCAP: 30,698,128–30,741,409, forward strand: 30,704,067–30,745,169, forward strandTMEM265: 30,737,880–30,745,196, forward strandPHKG2: 30,748,245–30,761,176, forward strandPHKG2CFAP119: 30,757,423–30,762,221, reverse strandCFAP119RNF40: 30,761,561–30,780,421, forward strandRNF40ZNF629: 30,778,456–30,787,214, reverse strandZNF629BCL7C: 30,818,695–30,894,302, reverse strandBCL7CCTF1: 30,896,607–30,903,547, forward strandCTF1FBXL19: 30,923,055–30,948,783, forward strandFBXL19ORAI3: 30,949,055–30,956,511, forward strandORAI3SETD1A: 30,957,754–30,984,664, forward strandSETD1AHSD3B7: 30,985,029–30,989,154, forward strandHSD3B7STX1B: 30,989,256–31,010,897, reverse strandSTX1BSTX4: 31,032,889–31,042,975, forward strandSTX4ZNF668: 31,059,772–31,074,240, reverse strandZNF668ZNF646: 31,074,394–31,084,196, forward strandZNF646PRSS53: 31,083,437–31,089,628, reverse strandPRSS53: 31,083,439–31,094,956, reverse strandVKORC1: 31,090,260–31,095,980, reverse strandBCKDK: 31,106,107–31,113,464, forward strandKAT8: 31,114,489–31,131,396, forward strandPRSS8: 31,131,433–31,135,727, reverse strandPRSS8PRSS36: 31,138,926–31,150,213, reverse strandPRSS36FUS: 31,180,131–31,196,963, forward strandFUSPYCARD: 31,201,486–31,203,450, reverse strandPYCARDTRIM72: 31,214,017–31,231,537, forward strandTRIM72PYDC1: 31,215,962–31,217,162, reverse strandPYDC1ITGAM: 31,259,954–31,332,892, forward strandITGAMITGAX: 31,355,134–31,382,999, forward strandITGAXITGAD: 31,393,258–31,426,505, forward strandITGADCOX6A2: 31,427,731–31,428,433, reverse strandCOX6A2ZNF843: 31,432,593–31,444,323, reverse strandZNF843ARMC5: 31,458,080–31,467,172, forward strandARMC5Diagram of SETD1A: 19 exons on the forward strand of chromosome 16Exon 2: 2 known disease-causing sitesExon 3: 1 known disease-causing siteExon 4: 2 known disease-causing sitesExon 5: 2 known disease-causing sitesExon 7: 5 known disease-causing sitesExon 8: 7 known disease-causing sitesExon 9: 3 known disease-causing sitesExon 10: 3 known disease-causing sitesExon 12: 2 known disease-causing sitesExon 13: 1 known disease-causing siteExon 14: 2 known disease-causing sitesExon 15: 1 known disease-causing siteExon 16: 2 known disease-causing sitesExon 17: 2 known disease-causing sitesExon 19: 1 known disease-causing siteExon 1: 30,957,754–30,957,964, 211 basesExon 2: 30,958,717–30,958,881, 165 basesExon 3: 30,959,091–30,959,186, 96 basesExon 4: 30,961,267–30,961,537, 271 basesExon 5: 30,963,433–30,963,554, 122 basesExon 6: 30,964,094–30,964,323, 230 basesExon 7: 30,964,612–30,965,461, 850 basesExon 8: 30,965,601–30,966,386, 786 basesExon 9: 30,966,884–30,967,060, 177 basesExon 10: 30,967,501–30,967,588, 88 basesExon 11: 30,969,305–30,969,462, 158 basesExon 12: 30,969,602–30,969,689, 88 basesExon 13: 30,971,378–30,971,719, 342 basesExon 14: 30,979,145–30,980,194, 1,050 basesExon 15: 30,980,485–30,980,657, 173 basesExon 16: 30,980,739–30,980,849, 111 basesExon 17: 30,981,061–30,981,180, 120 basesExon 18: 30,983,635–30,983,772, 138 basesExon 19: 30,983,850–30,984,664, 815 bases151015195′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 6 kb of the gene's 26.9 kb; 5,124 of those bases code for the protein.

How a genome test reads SETD1A

39

positions in SETD1A 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 26.9 kb of SETD1A, introns included, not only the 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.
  • 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.). SETD1A gene: SET domain containing 1A, histone lysine methyltransferase. Retrieved 16 October 2026, from https://dantelabs.com/genes/setd1a

Vancouver

Dante Labs. SETD1A gene: SET domain containing 1A, histone lysine methyltransferase [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/setd1a

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