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NM_000092.5(COL4A4):c.4715C>T (p.Pro1572Leu) AND not specified

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Feb 14, 2023
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000825912.6

Allele description [Variation Report for NM_000092.5(COL4A4):c.4715C>T (p.Pro1572Leu)]

NM_000092.5(COL4A4):c.4715C>T (p.Pro1572Leu)

Gene:
COL4A4:collagen type IV alpha 4 chain [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2q36.3
Genomic location:
Preferred name:
NM_000092.5(COL4A4):c.4715C>T (p.Pro1572Leu)
HGVS:
  • NC_000002.12:g.227008112G>A
  • NG_011592.1:g.161448C>T
  • NM_000092.5:c.4715C>TMANE SELECT
  • NP_000083.3:p.Pro1572Leu
  • NP_000083.3:p.Pro1572Leu
  • LRG_231t1:c.4715C>T
  • LRG_231:g.161448C>T
  • LRG_231p1:p.Pro1572Leu
  • NC_000002.11:g.227872828G>A
  • NM_000092.4:c.4715C>T
  • P53420:p.Pro1572Leu
Protein change:
P1572L; PRO1572LEU
Links:
UniProtKB: P53420#VAR_008155; OMIM: 120131.0006; dbSNP: rs121912863
NCBI 1000 Genomes Browser:
rs121912863
Molecular consequence:
  • NM_000092.5:c.4715C>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000967397Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
criteria provided, single submitter

(LMM Criteria)		Uncertain significance
(Mar 1, 2019) 		germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

SCV003844672Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Uncertain significance
(Feb 14, 2023) 		germlineclinical testing

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

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown11not providednot providednot providedclinical testing

Citations

PubMed

Whole exome sequencing reveals novel COL4A3 and COL4A4 mutations and resolves diagnosis in Chinese families with kidney disease.

Lin F, Bian F, Zou J, Wu X, Shan J, Lu W, Yao Y, Jiang G, Gale DP.

BMC Nephrol. 2014 Nov 7;15:175. doi: 10.1186/1471-2369-15-175.

PubMed [citation]
PMID:
25381091
PMCID:
PMC4233041

Genotype-phenotype correlations in 17 Chinese patients with autosomal recessive Alport syndrome.

Zhang Y, Wang F, Ding J, Zhang H, Zhao D, Yu L, Xiao H, Yao Y, Zhong X, Wang S.

Am J Med Genet A. 2012 Sep;158A(9):2188-93. doi: 10.1002/ajmg.a.35528. Epub 2012 Aug 6.

PubMed [citation]
PMID:
22887978
See all PubMed Citations (5)

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000967397.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (4)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not provided1not provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV003844672.1

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

Description

Variant summary: COL4A4 c.4715C>T (p.Pro1572Leu) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00016 in 248514 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in COL4A4 causing Alport Syndrome, Autosomal Recessive (0.00016 vs 0.0016), allowing no conclusion about variant significance. c.4715C>T has been reported in the literature in individuals affected with Alport Syndrome, Autosomal Recessive. These reports do not provide unequivocal conclusions about association of the variant with Alport Syndrome, Autosomal Recessive. Five clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation (likely benign n=1, VUS n=4). Based on the evidence outlined above, the variant was classified as uncertain significance.

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

Last Updated: Apr 20, 2025