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Gene

SEC61A1

SEC61 translocon subunit alpha 1

Summary

Cytogenetic location
3q21.3
Coordinates
Chromosome 3: 128,052,437–128,071,683 (GRCh38)
Exons
12 exons across 19.2 kb
Protein
476 amino acids
Inheritance
Autosomal dominant
MANE Select transcript
ENST00000243253.8NM_013336.4
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

  • Autosomal Dominant Tubulointerstitial Kidney Disease

    • Familial Juvenile Hyperuricemic NephropathyAutosomal dominant

      A dominantly inherited tubulointerstitial kidney disease, most often caused by UMOD variants (and also REN or SEC61A1), with high uric acid, early gout and gradual loss of kidney function.

      • 2 GenCC submitters rate it definitive or strong
      What knowing changes

      Knowing supports kidney function monitoring, gout treatment and careful evaluation of related living kidney donors; the REN form may respond to fludrocortisone.

  • Common Variable Immunodeficiency (Monogenic CVID)

    • Common variable immunodeficiency

      Low IgG with low IgA and/or IgM and poor vaccine responses; single-gene forms include NFKB1, NFKB2, ICOS, CD19, CD81, CR2, IKZF1, IRF2BP2, SEC61A1 and TNFRSF13B (TACI).

      • 1 GenCC submitter rates it definitive or strong
      What knowing changes

      Immunoglobulin replacement and early treatment of infections are standard; a genetic cause can guide monitoring for autoimmunity, lymphoma and lung disease, and some forms (such as LRBA deficiency) respond to targeted therapy.

Broader groupings

  • Other Inborn Errors of Immunity

    • Inborn error of immunity

      One of 114 genes linked to it

      Inherited disorders of the immune system caused by changes in single genes, affecting how the body fights infection or regulates inflammation.

      • 1 GenCC submitter rates it definitive or strong
    • Immunodeficiency Disease

      One of 170 genes linked to it

      Disease in which there is a deficiency or defect in the mechanisms of immunity, either cellular or humoral.

      • 1 GenCC submitter rates it definitive or strong
      What knowing changes

      HSCT for SCID and severe PIDs; immunoglobulin replacement (IVIG/SCIG) for antibody deficiencies; leniolisib (Joenja, FDA 2023) for APDS; gene therapy for ADA-SCID; abatacept for CTLA4/LRBA deficiency; prophylactic antibiotics; G-CSF for CGD

Inheritance

Autosomal dominant
One changed copy, from either parent, is enough. A parent who has one passes it on to each child with a one-in-two chance.

How SEC61A1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 3, with a bracket where SEC61A1 sits. SEC61A1 and 10 genes near it on chromosome 3, from 127,562,060 to 128,562,059.Chromosome 33q21.3p26.3p26.2p26.1p25.3p25.2p25.1p24.3p24.2p24.1p23p22.3p22.2p22.1p21.33p21.32p21.31p21.2p21.1p14.3p14.2p14.1p13p12.3p12.2p12.1p11.2p11.1q11.1q11.2q12.1q12.2q12.3q13.11q13.12q13.13q13.2q13.31q13.32q13.33q21.1q21.2q21.3q22.1q22.2q22.3q23q24q25.1q25.2q25.31q25.32q25.33q26.1q26.2q26.31q26.32q26.33q27.1q27.2q27.3q28q29127.6 Mb127.8 Mb128 Mb128.2 Mb128.4 MbTPRA1: 127,571,232–127,598,318, reverse strandTPRA1MCM2: 127,598,223–127,622,442, forward strandMCM2PODXL2: 127,629,143–127,672,810, forward strandPODXL2ABTB1: 127,672,894–127,683,197, forward strandABTB1MGLL: 127,689,062–128,052,190, reverse strandMGLLKBTBD12: 127,915,207–127,989,100, forward strandKBTBD12SEC61A1: 128,052,437–128,071,683, forward strandSEC61A1RUVBL1: 128,063,024–128,153,914, reverse strandRUVBL1EEFSEC: 128,153,174–128,427,044, forward strandEEFSECDNAJB8: 128,462,437–128,466,968, reverse strandDNAJB8GATA2: 128,479,423–128,493,208, reverse strandGATA2Diagram of SEC61A1: 12 exons on the forward strand of chromosome 3Exon 4: 1 known disease-causing siteExon 5: 1 known disease-causing siteExon 7: 1 known disease-causing siteExon 1: 128,052,437–128,052,559, 123 basesExon 2: 128,052,835–128,052,902, 68 basesExon 3: 128,055,516–128,055,581, 66 basesExon 4: 128,055,673–128,055,751, 79 basesExon 5: 128,056,709–128,056,840, 132 basesExon 6: 128,060,102–128,060,211, 110 basesExon 7: 128,060,508–128,060,661, 154 basesExon 8: 128,064,877–128,065,037, 161 basesExon 9: 128,066,954–128,067,151, 198 basesExon 10: 128,067,421–128,067,612, 192 basesExon 11: 128,067,983–128,068,059, 77 basesExon 12: 128,069,476–128,071,683, 2,208 bases1246810125′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 19.2 kb; 1,431 of those bases code for the protein.

How a genome test reads SEC61A1

3

positions in SEC61A1 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 19.2 kb of SEC61A1, 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.). SEC61A1 gene: SEC61 translocon subunit alpha 1. Retrieved 16 October 2026, from https://dantelabs.com/genes/sec61a1

Vancouver

Dante Labs. SEC61A1 gene: SEC61 translocon subunit alpha 1 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/sec61a1

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