chr11-119067860-T-C

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate

The NM_021729.6(VPS11):​c.37T>C​(p.Phe13Leu) variant causes a missense change involving the alteration of a conserved nucleotide. 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 Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)

Consequence

VPS11
NM_021729.6 missense

Scores

7
1
1

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 7.77
Variant links:
Genes affected
VPS11 (HGNC:14583): (VPS11 core subunit of CORVET and HOPS complexes) Vesicle mediated protein sorting plays an important role in segregation of intracellular molecules into distinct organelles. Genetic studies in yeast have identified more than 40 vacuolar protein sorting (VPS) genes involved in vesicle transport to vacuoles. This gene encodes the human homolog of yeast class C Vps11 protein. The mammalian class C Vps proteins are predominantly associated with late endosomes/lysosomes, and like their yeast counterparts, may mediate vesicle trafficking steps in the endosome/lysosome pathway. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2014]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.884

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
VPS11NM_021729.6 linkc.37T>C p.Phe13Leu missense_variant Exon 1 of 16 ENST00000621676.5 NP_068375.3 Q9H270A0A087WXL6B7Z879

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
VPS11ENST00000621676.5 linkc.37T>C p.Phe13Leu missense_variant Exon 1 of 16 1 NM_021729.6 ENSP00000481126.1 A0A087WXL6
VPS11ENST00000614944 linkc.-209T>C 5_prime_UTR_variant Exon 1 of 16 2 ENSP00000481807.1 B7Z879
VPS11ENST00000622309.4 linkn.38T>C non_coding_transcript_exon_variant Exon 1 of 13 5

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
33

ClinVar

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

Submissions by phenotype

Inborn genetic diseases Uncertain:1
Oct 06, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.37T>C (p.F13L) alteration is located in exon 1 (coding exon 1) of the VPS11 gene. This alteration results from a T to C substitution at nucleotide position 37, causing the phenylalanine (F) at amino acid position 13 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
1.0
BayesDel_addAF
Pathogenic
0.62
D
BayesDel_noAF
Pathogenic
0.65
CADD
Pathogenic
28
DANN
Benign
0.89
FATHMM_MKL
Pathogenic
0.99
D
M_CAP
Uncertain
0.13
D
MetaRNN
Pathogenic
0.88
D
PrimateAI
Pathogenic
0.87
D
Sift4G
Pathogenic
0.0
D
Vest4
0.96
MVP
0.45
GERP RS
5.2
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
2.1
gMVP
0.90

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: chr11-118938571; API