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NM_001365902.3(NFIX):c.143T>A (p.Met48Lys) AND multiple conditions

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Apr 9, 2023
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV003766975.2

Allele description [Variation Report for NM_001365902.3(NFIX):c.143T>A (p.Met48Lys)]

NM_001365902.3(NFIX):c.143T>A (p.Met48Lys)

Gene:
NFIX:nuclear factor I X [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
19p13.13
Genomic location:
Preferred name:
NM_001365902.3(NFIX):c.143T>A (p.Met48Lys)
HGVS:
  • NC_000019.10:g.13025136T>A
  • NG_032925.2:g.34367T>A
  • NM_001271043.2:c.167T>A
  • NM_001271044.3:c.119T>A
  • NM_001365902.3:c.143T>AMANE SELECT
  • NM_001365982.2:c.143T>A
  • NM_001365983.2:c.2T>A
  • NM_001365984.2:c.140T>A
  • NM_001365985.2:c.140T>A
  • NM_001378404.1:c.119T>A
  • NM_001378405.1:c.191T>A
  • NM_002501.4:c.143T>A
  • NP_001257972.1:p.Met56Lys
  • NP_001257973.1:p.Met40Lys
  • NP_001352831.1:p.Met48Lys
  • NP_001352911.1:p.Met48Lys
  • NP_001352912.1:p.Met1Lys
  • NP_001352913.1:p.Met47Lys
  • NP_001352914.1:p.Met47Lys
  • NP_001365333.1:p.Met40Lys
  • NP_001365334.1:p.Met64Lys
  • NP_002492.2:p.Met48Lys
  • NC_000019.9:g.13135950T>A
  • NM_001271043.1:c.167T>A
  • NM_001365902.3:c.143T>A
  • NM_002501.3:c.143T>A
Protein change:
M1K
Links:
dbSNP: rs1555696484
NCBI 1000 Genomes Browser:
rs1555696484
Molecular consequence:
  • NM_001365983.2:c.2T>A - initiator_codon_variant - [Sequence Ontology: SO:0001582]
  • NM_001271043.2:c.167T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001271044.3:c.119T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001365902.3:c.143T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001365982.2:c.143T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001365983.2:c.2T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001365984.2:c.140T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001365985.2:c.140T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001378404.1:c.119T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001378405.1:c.191T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_002501.4:c.143T>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Marshall-Smith syndrome (MRSHSS)
Identifiers:
MONDO: MONDO:0011244; MedGen: C0265211; Orphanet: 561; OMIM: 602535
Name:
Malan overgrowth syndrome (MALNS)
Synonyms:
Sotos syndrome 2; MALAN SYNDROME
Identifiers:
MONDO: MONDO:0013885; MedGen: C3553660; Orphanet: 420179; OMIM: 614753

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004579658Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Likely pathogenic
(Apr 9, 2023) 		germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Benefits of clinical criteria and high-throughput sequencing for diagnosing children with syndromic craniosynostosis.

Tønne E, Due-Tønnessen BJ, Mero IL, Wiig US, Kulseth MA, Vigeland MD, Sheng Y, von der Lippe C, Tveten K, Meling TR, Helseth E, Heimdal KR.

Eur J Hum Genet. 2021 Jun;29(6):920-929. doi: 10.1038/s41431-020-00788-4. Epub 2020 Dec 7.

PubMed [citation]
PMID:
33288889
PMCID:
PMC8187391

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004579658.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

This variant is not present in population databases (gnomAD no frequency). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. ClinVar contains an entry for this variant (Variation ID: 452926). This variant is also known as c.143T>A p.(Met48Lys). This missense change has been observed in individual(s) with clinical features of Sotos-like syndrome (PMID: 33288889). In at least one individual the variant was observed to be de novo. This sequence change replaces methionine, which is neutral and non-polar, with lysine, which is basic and polar, at codon 56 of the NFIX protein (p.Met56Lys).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 3, 2024