NSD1 A2546T - GET-Evidence


NSD1 A2546T

(NSD1 Ala2546Thr)

Short summary

Benign, reported as a polymorphism.

Variant evidence

Polyphen 2 predicts “possibly damaging” effect

Functional -
Case/Control 4

Allele frequency is inconsistent with severe pathogenic effect

Familial -
Clinical importance
Severity -
Treatability -
Penetrance -


Low clinical importance, Uncertain benign

(The "low clinical importance, uncertain" qualifier is assigned automatically based on the above evidence and importance scores.)

Inheritance pattern


Summary of published research, and additional commentary


Allele frequency

  • A @ chr5:176722005: 2.5% (273/10748) in EVS
  • A @ chr5:176654610: 2.3% (3/128) in GET-Evidence
  • Frequency shown in summary reports: 2.5% (273/10748)


Türkmen S, Gillessen-Kaesbach G, Meinecke P, Albrecht B, Neumann LM, Hesse V, Palanduz S, Balg S, Majewski F, Fuchs S, Zschieschang P, Greiwe M, Mennicke K, Kreuz FR, Dehmel HJ, Rodeck B, Kunze J, Tinschert S, Mundlos S, Horn D. Mutations in NSD1 are responsible for Sotos syndrome, but are not a frequent finding in other overgrowth phenotypes. Eur J Hum Genet. 2003 Nov;11(11):858-65. PubMed PMID: 14571271.

Listed as a polymorphism.

Melchior L, Schwartz M, Duno M. dHPLC screening of the NSD1 gene identifies nine novel mutations--summary of the first 100 Sotos syndrome mutations. Ann Hum Genet. 2005 Mar;69(Pt 2):222-6. PubMed PMID: 15720303.

Listed as a known (previously reported) polymorphism.


hu72A81D - CGI sample GS01173-DNA_C02 from PGP sample 10366372
het A @ chr5:176722005


hu9385BA - CGI sample GS00253-DNA_E01_200_37
het A @ chr5:176722005


huB1FD55 - CGI sample GS01173-DNA_B07 from PGP sample 61499538
het A @ chr5:176722005


huBAAC98 - CGI sample GS01173-DNA_F02 from PGP sample 70008981
het A @ chr5:176722005


huFAF983 - CGI sample GS01175-DNA_F02 from PGP sample 95788191
het A @ chr5:176722005


GS19026 - var-GS19026-1100-36-ASM
het A @ chr5:176654611


Other external references

  • rs78247455
  • Score: 0.458 (possibly damaging)
    Web search results (4 hits -- see all)
  • European Journal of Human Genetics - Mutations in NSD1 are ...
    The European Journal of Human Genetics is the official Journal of the European Society of Human Genetics, publishing high-quality, original research papers, short ...
  • Table 1
    Sequence variants identified in the NSD1 gene in 88 patients with autism ... A2546T. 11 G/A [32, 52] 1 References are given only for variants without a RefSNP ...
  • Mutation analysis of the NSD1 gene in patients with autism ...
    We screened the NSD1 gene for mutations and deletions in 88 patients ... Dosage analysis of NSD1 was carried out using multiplex ligation-dependent probe ...

Other in silico analyses

  • NBLOSUM100 score = 1
  • GET-Evidence autoscore = 4

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Gene search

"GENE" or "GENE A123C":

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