rs77606940

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_021075.4(NDUFV3):​c.11C>A​(p.Pro4Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000361 in 1,386,094 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000036 ( 0 hom. )

Consequence

NDUFV3
NM_021075.4 missense

Scores

19

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.215
Variant links:
Genes affected
NDUFV3 (HGNC:7719): (NADH:ubiquinone oxidoreductase subunit V3) The protein encoded by this gene is one of at least forty-one subunits that make up the NADH-ubiquinone oxidoreductase complex. This complex is part of the mitochondrial respiratory chain and serves to catalyze the rotenone-sensitive oxidation of NADH and the reduction of ubiquinone. The encoded protein is one of three proteins found in the flavoprotein fraction of the complex. The specific function of the encoded protein is unknown. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.10628149).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NDUFV3NM_021075.4 linkc.11C>A p.Pro4Gln missense_variant Exon 1 of 4 ENST00000354250.7 NP_066553.3 P56181-2
NDUFV3NM_001001503.2 linkc.11C>A p.Pro4Gln missense_variant Exon 1 of 3 NP_001001503.1 P56181-1
NDUFV3XM_011529586.3 linkc.11C>A p.Pro4Gln missense_variant Exon 1 of 5 XP_011527888.1
NDUFV3XM_017028359.2 linkc.11C>A p.Pro4Gln missense_variant Exon 1 of 4 XP_016883848.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NDUFV3ENST00000354250.7 linkc.11C>A p.Pro4Gln missense_variant Exon 1 of 4 1 NM_021075.4 ENSP00000346196.2 P56181-2
NDUFV3ENST00000340344.4 linkc.11C>A p.Pro4Gln missense_variant Exon 1 of 3 1 ENSP00000342895.3 P56181-1
NDUFV3ENST00000460740.1 linkn.24C>A non_coding_transcript_exon_variant Exon 1 of 2 2
NDUFV3ENST00000460259.1 linkn.572-3583C>A intron_variant Intron 3 of 5 2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
0.00000361
AC:
5
AN:
1386094
Hom.:
0
Cov.:
31
AF XY:
0.00000146
AC XY:
1
AN XY:
684068
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000126
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000371
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.096
BayesDel_addAF
Benign
-0.24
T
BayesDel_noAF
Benign
-0.59
CADD
Benign
0.93
DANN
Benign
0.64
DEOGEN2
Benign
0.0054
.;T
Eigen
Benign
-0.90
Eigen_PC
Benign
-1.0
FATHMM_MKL
Benign
0.055
N
LIST_S2
Benign
0.44
T;T
M_CAP
Benign
0.0086
T
MetaRNN
Benign
0.11
T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
0.69
N;N
PrimateAI
Benign
0.45
T
PROVEAN
Benign
-0.59
N;N
REVEL
Benign
0.025
Sift
Benign
0.31
T;D
Sift4G
Benign
0.13
T;T
Polyphen
0.74
P;P
Vest4
0.16
MutPred
0.27
Loss of catalytic residue at P4 (P = 0.0141);Loss of catalytic residue at P4 (P = 0.0141);
MVP
0.33
MPC
0.16
ClinPred
0.19
T
GERP RS
-0.21
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.034
gMVP
0.12

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs77606940; hg19: chr21-44313454; API