14-100727093-C-T

Variant names:

• chr14-100727093-C-T
• NM_003836.7:c.25C>T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_003836.7(DLK1):​c.25C>T​(p.Arg9Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000694 in 1,441,480 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: DLK1 NM_003836.7 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.592

Genes affected

DLK1 (HGNC:2907): (delta like non-canonical Notch ligand 1) This gene encodes a transmembrane protein that contains multiple epidermal growth factor repeats that functions as a regulator of cell growth. The encoded protein is involved in the differentiation of several cell types including adipocytes. This gene is located in a region of chromosome 14 frequently showing unparental disomy, and is imprinted and expressed from the paternal allele. A single nucleotide variant in this gene is associated with child and adolescent obesity and shows polar overdominance, where heterozygotes carrying an active paternal allele express the phenotype, while mutant homozygotes are normal. [provided by RefSeq, Nov 2015]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DLK1	NM_003836.7	c.25C>T	p.Arg9Cys	missense_variant	Exon 1 of 5	ENST00000341267.9	NP_003827.4
DLK1	NM_001317172.2	c.25C>T	p.Arg9Cys	missense_variant	Exon 1 of 6		NP_001304101.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DLK1	ENST00000341267.9	c.25C>T	p.Arg9Cys	missense_variant	Exon 1 of 5	1	NM_003836.7	ENSP00000340292.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.94e-7 AC: 1 AN: 1441480 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 717242

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: 0.0000197

Gnomad4 NFE exome AF: 0.00

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	0.27
BayesDel_addAF	Benign	-0.00058	T
BayesDel_noAF	Benign	-0.24
CADD	Uncertain	25
DANN	Uncertain	1.0
DEOGEN2	Benign	0.089	T;T;T;.;.
Eigen	Benign	-0.0052
Eigen_PC	Benign	-0.075
FATHMM_MKL	Benign	0.31	N
LIST_S2	Benign	0.67	T;.;T;T;T
M_CAP	Pathogenic	0.94	D
MetaRNN	Uncertain	0.45	T;T;T;T;T
MetaSVM	Uncertain	-0.26	T
MutationAssessor	Benign	1.4	.;L;L;L;.
PrimateAI	Uncertain	0.75	T
PROVEAN	Benign	0.76	N;N;.;N;N
REVEL	Uncertain	0.35
Sift	Benign	0.088	T;T;.;T;T
Sift4G	Uncertain	0.039	D;T;.;T;D
Polyphen		1.0	.;D;D;D;.
Vest4		0.20, 0.21, 0.32
MutPred		0.54		Gain of catalytic residue at V10 (P = 0.0073);Gain of catalytic residue at V10 (P = 0.0073);Gain of catalytic residue at V10 (P = 0.0073);Gain of catalytic residue at V10 (P = 0.0073);Gain of catalytic residue at V10 (P = 0.0073);
MVP		0.89
MPC		0.95
ClinPred		0.79	D
GERP RS		0.92
RBP_binding_hub_radar		0.92
RBP_regulation_power_radar		2.2
Varity_R		0.084
gMVP		0.75

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: chr14-101193430;