Variant 5-74635951-T-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_003633.4(ENC1):c.535A>T(p.Ile179Phe) variant causes a missense change. The variant allele was found at a frequency of 0.00000137 in 1,461,842 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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: 0.0000014 ( 0 hom. )

Consequence

ENC1
NM_003633.4 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 6.18

Variant links:

Genes affected

ENC1 (HGNC:3345): (ectodermal-neural cortex 1) This gene encodes a member of the kelch-related family of actin-binding proteins. The encoded protein plays a role in the oxidative stress response as a regulator of the transcription factor Nrf2, and expression of this gene may play a role in malignant transformation. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Feb 2012]

ENC1 links:

ENC1 (HGNC:):

ENC1 links:

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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, 0.922

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ENC1	NM_003633.4 linkuse as main transcript	c.535A>T	p.Ile179Phe	missense_variant	2/3	ENST00000302351.9	NP_003624.1	O14682-1Q53XS2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
ENC1	ENST00000302351.9 linkuse as main transcript	c.535A>T	p.Ile179Phe	missense_variant	2/3	1	NM_003633.4	ENSP00000306356.4	O14682-1
ENC1	ENST00000618628.4 linkuse as main transcript	c.535A>T	p.Ile179Phe	missense_variant	3/4	5		ENSP00000479101.1	O14682-1
ENC1	ENST00000651128.1 linkuse as main transcript	c.535A>T	p.Ile179Phe	missense_variant	3/4			ENSP00000499185.1	O14682-1
ENC1	ENST00000510316.5 linkuse as main transcript	c.316A>T	p.Ile106Phe	missense_variant	2/3	2		ENSP00000423804.1	O14682-2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000137

AC:

AN:

1461842

Hom.:

Cov.:

AF XY:

0.00000138

AC XY:

AN XY:

727210

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:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000180

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

Alfa

AF:

0.0000936

Hom.:

Bravo

AF:

0.00000378

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Aug 05, 2024

The c.535A>T (p.I179F) alteration is located in exon 2 (coding exon 1) of the ENC1 gene. This alteration results from a A to T substitution at nucleotide position 535, causing the isoleucine (I) at amino acid position 179 to be replaced by a phenylalanine (F). 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

Uncertain

0.37

BayesDel_addAF

Pathogenic

0.33

BayesDel_noAF

Pathogenic

0.24

CADD

Uncertain

DANN

Uncertain

0.99

DEOGEN2

Uncertain

0.47

T;T;.;T

Eigen

Uncertain

0.50

Eigen_PC

Uncertain

0.54

FATHMM_MKL

Uncertain

0.96

LIST_S2

Uncertain

0.94

.;D;D;.

M_CAP

Benign

0.078

MetaRNN

Pathogenic

0.92

D;D;D;D

MetaSVM

Benign

-0.37

MutationAssessor

Benign

1.2

L;L;.;L

PrimateAI

Pathogenic

0.80

PROVEAN

Uncertain

-3.5

D;.;D;D

REVEL

Pathogenic

0.80

Sift

Uncertain

0.0010

D;.;D;D

Sift4G

Uncertain

0.011

D;D;D;D

Polyphen

0.91

P;P;.;P

Vest4

0.84

MutPred

0.77

Gain of ubiquitination at K181 (P = 0.07);Gain of ubiquitination at K181 (P = 0.07);.;Gain of ubiquitination at K181 (P = 0.07);

MVP

0.75

MPC

1.8

ClinPred

0.98

GERP RS

4.8

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.77

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over