chrX-108440128-G-T

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate

The NM_033380.3(COL4A5):​c.3G>T​(p.Met1?) variant causes a start lost change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★).

Frequency

Genomes: not found (cov: 21)

Consequence

COL4A5
NM_033380.3 start_lost

Scores

5
4
5

Clinical Significance

Pathogenic criteria provided, single submitter P:1

Conservation

PhyloP100: 4.04
Variant links:
Genes affected
COL4A5 (HGNC:2207): (collagen type IV alpha 5 chain) This gene encodes one of the six subunits of type IV collagen, the major structural component of basement membranes. Mutations in this gene are associated with X-linked Alport syndrome, also known as hereditary nephritis. Like the other members of the type IV collagen gene family, this gene is organized in a head-to-head conformation with another type IV collagen gene so that each gene pair shares a common promoter. Alternatively spliced transcript variants have been identified for this gene. [provided by RefSeq, Aug 2010]

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ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 12 ACMG points.

PVS1
Start lost variant, no new inframe start found.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant X-108440128-G-T is Pathogenic according to our data. Variant chrX-108440128-G-T is described in ClinVar as [Pathogenic]. Clinvar id is 2770173.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-108440128-G-T is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
COL4A5NM_033380.3 linkuse as main transcriptc.3G>T p.Met1? start_lost 1/53 ENST00000328300.11 NP_203699.1
COL4A5NM_000495.5 linkuse as main transcriptc.3G>T p.Met1? start_lost 1/51 NP_000486.1
COL4A5XM_047441811.1 linkuse as main transcriptc.3G>T p.Met1? start_lost 1/42 XP_047297767.1
COL4A5XM_047441810.1 linkuse as main transcriptc.-374G>T 5_prime_UTR_variant 1/54 XP_047297766.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
COL4A5ENST00000328300.11 linkuse as main transcriptc.3G>T p.Met1? start_lost 1/531 NM_033380.3 ENSP00000331902 P29400-2

Frequencies

GnomAD3 genomes
Cov.:
21
GnomAD4 exome
Cov.:
29
GnomAD4 genome
Cov.:
21

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJun 05, 2023For these reasons, this variant has been classified as Pathogenic. This variant disrupts a region of the COL4A5 protein in which other variant(s) (p.Gly54Arg) have been determined to be pathogenic (Invitae). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. Disruption of the initiator codon has been observed in individuals with Alport syndrome (PMID: 24033287; Invitae). This variant is not present in population databases (gnomAD no frequency). This sequence change affects the initiator methionine of the COL4A5 mRNA. The next in-frame methionine is located at codon 109. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
0.74
D
BayesDel_noAF
Pathogenic
0.51
CADD
Benign
21
DANN
Uncertain
0.99
DEOGEN2
Benign
0.12
.;T
FATHMM_MKL
Benign
0.73
D
LIST_S2
Uncertain
0.90
D;D
M_CAP
Pathogenic
0.99
D
MetaRNN
Pathogenic
0.99
D;D
MetaSVM
Uncertain
0.47
D
MutationTaster
Benign
1.0
D;D
PROVEAN
Benign
-0.84
N;N
REVEL
Uncertain
0.62
Sift
Benign
0.031
D;D
Sift4G
Pathogenic
0.0
D;D
Polyphen
0.53
.;P
Vest4
0.88
MutPred
0.90
Loss of MoRF binding (P = 0.078);Loss of MoRF binding (P = 0.078);
MVP
1.0
ClinPred
0.96
D
GERP RS
4.7
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.55
gMVP
0.89

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chrX-107683358; API