NM_000670.5:c.1042C>G

Variant names:

• chr4-99126670-G-C
• NM_000670.5:c.1042C>G

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_000670.5(ADH4):​c.1042C>G​(p.Leu348Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L348Q) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ADH4 NM_000670.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.629
• Publications: 0 publications found

Genes affected

ADH4 (HGNC:252): (alcohol dehydrogenase 4 (class II), pi polypeptide) This gene encodes class II alcohol dehydrogenase 4 pi subunit, which is a member of the alcohol dehydrogenase family. Members of this enzyme family metabolize a wide variety of substrates, including ethanol, retinol, other aliphatic alcohols, hydroxysteroids, and lipid peroxidation products. Class II alcohol dehydrogenase is a homodimer composed of 2 pi subunits. It exhibits a high activity for oxidation of long-chain aliphatic alcohols and aromatic alcohols and is less sensitive to pyrazole. This gene is localized to chromosome 4 in the cluster of alcohol dehydrogenase genes. [provided by RefSeq, Jul 2008]

ENSG00000246090 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.07325983).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADH4	NM_000670.5	c.1042C>G	p.Leu348Val	missense_variant	Exon 8 of 9	ENST00000265512.12	NP_000661.2
ADH4	NM_001306171.2	c.1099C>G	p.Leu367Val	missense_variant	Exon 9 of 10		NP_001293100.1
ADH4	NM_001306172.2	c.1099C>G	p.Leu367Val	missense_variant	Exon 9 of 10		NP_001293101.1
LOC100507053	NR_037884.1	n.429-6885G>C		intron_variant	Intron 1 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADH4	ENST00000265512.12	c.1042C>G	p.Leu348Val	missense_variant	Exon 8 of 9	1	NM_000670.5	ENSP00000265512.7

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Jun 24, 2022

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1042C>G (p.L348V) alteration is located in exon 8 (coding exon 8) of the ADH4 gene. This alteration results from a C to G substitution at nucleotide position 1042, causing the leucine (L) at amino acid position 348 to be replaced by a valine (V). 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	Benign	0.13
BayesDel_addAF	Benign	-0.30	T
BayesDel_noAF	Benign	-0.67
CADD	Benign	13
DANN	Uncertain	0.99
DEOGEN2	Benign	0.029	.;T;T;.
Eigen	Benign	-0.77
Eigen_PC	Benign	-0.71
FATHMM_MKL	Benign	0.13	N
LIST_S2	Uncertain	0.87	.;D;D;D
M_CAP	Benign	0.0048	T
MetaRNN	Benign	0.073	T;T;T;T
MetaSVM	Benign	-0.92	T
MutationAssessor	Benign	1.4	.;.;L;.
PhyloP100		-0.63
PrimateAI	Benign	0.30	T
PROVEAN	Benign	-1.4	N;.;N;N
REVEL	Benign	0.060
Sift	Benign	0.40	T;.;T;T
Sift4G	Benign	0.49	T;T;T;T
Polyphen		0.085	B;.;B;B
Vest4		0.11
MutPred		0.54		.;Gain of methylation at K344 (P = 0.1038);Gain of methylation at K344 (P = 0.1038);.;
MVP		0.23
MPC		0.27
ClinPred		0.21	T
GERP RS		1.9
Varity_R		0.19
gMVP		0.62
Mutation Taster		=80/20	polymorphism

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

Other links and lift over

hg19: chr4-100047821;