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NM_003937.3(KYNU):c.616G>A (p.Glu206Lys) AND Vertebral, cardiac, renal, and limb defects syndrome 2

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Mar 6, 2024
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV003883467.1

Allele description [Variation Report for NM_003937.3(KYNU):c.616G>A (p.Glu206Lys)]

NM_003937.3(KYNU):c.616G>A (p.Glu206Lys)

Gene:
KYNU:kynureninase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2q22.2
Genomic location:
Preferred name:
NM_003937.3(KYNU):c.616G>A (p.Glu206Lys)
HGVS:
  • NC_000002.12:g.142960657G>A
  • NG_023254.1:g.88032G>A
  • NM_001032998.2:c.616G>A
  • NM_001199241.2:c.616G>A
  • NM_003937.3:c.616G>AMANE SELECT
  • NP_001028170.1:p.Glu206Lys
  • NP_001186170.1:p.Glu206Lys
  • NP_003928.1:p.Glu206Lys
  • NC_000002.11:g.143718226G>A
Protein change:
E206K; GLU206LYS
Links:
OMIM: 605197.0008; dbSNP: rs765122670
NCBI 1000 Genomes Browser:
rs765122670
Molecular consequence:
  • NM_001032998.2:c.616G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001199241.2:c.616G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_003937.3:c.616G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Vertebral, cardiac, renal, and limb defects syndrome 2
Synonyms:
KYNURENINASE DEFICIENCY, COMPLETE; CONGENITAL NAD DEFICIENCY DISORDER 2
Identifiers:
MONDO: MONDO:0060555; MedGen: C4540014; OMIM: 617661

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004697940OMIM
no assertion criteria provided
Pathogenic
(Mar 6, 2024) 		germlineliterature only

Szot, J. O., Slavotinek, A., Chong, K., Brandau, O., Nezarati, M., Cueto-Gonzalez, A. M., Patel, M. S., Devine, W. P., Rego, S., Acyinena, A. P., Shannon, P., Myles-Reid, D., and 17 others New cases that expand the genotypic and phenotypic spectrum of congenital NAD deficiency disorder. Hum. Mutat. 42: 862-876, 2021.

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Details of each submission

From OMIM, SCV004697940.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature onlynot provided

Description

In a patient, born of unrelated Sri Lankan parents (family 5), with vertebral, cardiac, renal, and limb defects syndrome-2 (VCRL2; 617661), Szot et al. (2021) identified a homozygous c.616G-A transition (c.616G-A, NM_003937.3) in the KYNU gene resulting in a glu206-to-lys (E206K) substitution. The mutation was identified by trio whole-exome sequencing and the parents were shown to be mutation carriers. The mutation was present in the gnomAD database at an allele frequency of 0.0000199. Yeast with a homozygous knockout for bna5, the yeast ortholog of KYNU, were transformed with plasmids containing KYNU with the E206K mutation or with wildtype KYNU. The yeast transformed with the mutant KYNU plasmid had a reduced NAD level compared to wildtype.

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

Last Updated: Mar 16, 2024