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NM_020347.4(LZTFL1):c.505A>T (p.Lys169Ter) AND Bardet-Biedl syndrome 17

Germline classification:
Pathogenic (1 submission)
Last evaluated:
May 2, 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:
RCV004527271.1

Allele description [Variation Report for NM_020347.4(LZTFL1):c.505A>T (p.Lys169Ter)]

NM_020347.4(LZTFL1):c.505A>T (p.Lys169Ter)

Gene:
LZTFL1:leucine zipper transcription factor like 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3p21.31
Genomic location:
Preferred name:
NM_020347.4(LZTFL1):c.505A>T (p.Lys169Ter)
Other names:
K169*
HGVS:
  • NC_000003.12:g.45831090T>A
  • NG_033917.1:g.89635A>T
  • NM_001276378.2:c.454A>T
  • NM_001276379.2:c.493A>T
  • NM_001386451.1:c.454A>T
  • NM_001386452.1:c.505A>T
  • NM_001405920.1:c.529A>T
  • NM_001405921.1:c.493A>T
  • NM_001405922.1:c.454A>T
  • NM_001405923.1:c.454A>T
  • NM_001405924.1:c.457-100A>T
  • NM_001405925.1:c.529A>T
  • NM_001405926.1:c.454A>T
  • NM_001405927.1:c.454A>T
  • NM_001405928.1:c.454A>T
  • NM_020347.4:c.505A>TMANE SELECT
  • NP_001263307.1:p.Lys152Ter
  • NP_001263308.1:p.Lys165Ter
  • NP_001373380.1:p.Lys152Ter
  • NP_001373381.1:p.Lys169Ter
  • NP_001392849.1:p.Lys177Ter
  • NP_001392850.1:p.Lys165Ter
  • NP_001392851.1:p.Lys152Ter
  • NP_001392852.1:p.Lys152Ter
  • NP_001392854.1:p.Lys177Ter
  • NP_001392855.1:p.Lys152Ter
  • NP_001392856.1:p.Lys152Ter
  • NP_001392857.1:p.Lys152Ter
  • NP_065080.1:p.Lys169Ter
  • NC_000003.11:g.45872582T>A
  • NR_075080.2:n.508A>T
  • NR_175976.1:n.508A>T
Protein change:
K152*; LYS169TER
Links:
OMIM: 606568.0004
Molecular consequence:
  • NM_001405924.1:c.457-100A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NR_075080.2:n.508A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_175976.1:n.508A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001276378.2:c.454A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001276379.2:c.493A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001386451.1:c.454A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001386452.1:c.505A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001405920.1:c.529A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001405921.1:c.493A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001405922.1:c.454A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001405923.1:c.454A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001405925.1:c.529A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001405926.1:c.454A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001405927.1:c.454A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001405928.1:c.454A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_020347.4:c.505A>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Bardet-Biedl syndrome 17 (BBS17)
Identifiers:
MONDO: MONDO:0014445; MedGen: C3714980; Orphanet: 110; OMIM: 615994

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV005040762OMIM
no assertion criteria provided
Pathogenic
(May 2, 2024) 		germlineliterature only

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

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

Citations

PubMed

Biallelic Variants in Seven Different Genes Associated with Clinically Suspected Bardet-Biedl Syndrome.

Nawaz H, Mujahid, Khan SA, Bibi F, Waqas A, Bari A, Fardous, Khan N, Muhammad N, Khan A, Paracha SA, Alam Q, Kamal MA, Rafeeq MM, Muhammad N, Haq FU, Khan S, Mahmood A, Khan S, Umair M.

Genes (Basel). 2023 May 19;14(5). doi: 10.3390/genes14051113.

PubMed [citation]
PMID:
37239474
PMCID:
PMC10217928

Details of each submission

From OMIM, SCV005040762.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)

Description

By whole-exome sequencing in a 15-year-old girl (family D) with Bardet-Biedl syndrome (BBS17; 615994), Nawaz et al. (2023) identified homozygosity for a c.505A-T transversion (c.505A-T, NM_020347.4) in the LZTFL1 gene, resulting in a lys169-to-ter (K169X) substitution. Sanger sequencing confirmed that her unaffected consanguineous parents and her unaffected brother were heterozygous for the mutation. The variant was predicted to produce a truncated protein of only 168 amino acids, which would activate nonsense-mediated decay machinery resulting in degradation of the mutant mRNA and absence of protein.

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

Last Updated: May 19, 2024