1-117025667-G-A

Variant names:

• chr1-117025667-G-A
• NM_001256106.3:c.2587G>A

Variant summary

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

The NM_001256106.3(CD101):​c.2587G>A​(p.Val863Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: CD101 NM_001256106.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 2.23

Genes affected

CD101 (HGNC:5949): (CD101 molecule) Predicted to enable hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides. Predicted to be involved in cell surface receptor signaling pathway. Predicted to act upstream of or within positive regulation of myeloid leukocyte differentiation. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

CD101-AS1 (HGNC:55665): (CD101 antisense RNA 1)

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
CD101	NM_001256106.3	c.2587G>A	p.Val863Met	missense_variant	Exon 8 of 10	ENST00000682167.1	NP_001243035.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD101	ENST00000682167.1	c.2587G>A	p.Val863Met	missense_variant	Exon 8 of 10		NM_001256106.3	ENSP00000508039.1
CD101	ENST00000369470.1	c.2587G>A	p.Val863Met	missense_variant	Exon 8 of 10	1		ENSP00000358482.1
CD101	ENST00000256652.8	c.2587G>A	p.Val863Met	missense_variant	Exon 8 of 9	2		ENSP00000256652.4
CD101-AS1	ENST00000445523.1	n.1629C>T		non_coding_transcript_exon_variant	Exon 4 of 4	2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Mar 02, 2023

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.2587G>A (p.V863M) alteration is located in exon 8 (coding exon 8) of the CD101 gene. This alteration results from a G to A substitution at nucleotide position 2587, causing the valine (V) at amino acid position 863 to be replaced by a methionine (M). 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	0.21
BayesDel_addAF	Benign	-0.023	T
BayesDel_noAF	Benign	-0.27
CADD	Benign	21
DANN	Uncertain	1.0
DEOGEN2	Benign	0.13	T;T
Eigen	Uncertain	0.39
Eigen_PC	Uncertain	0.30
FATHMM_MKL	Uncertain	0.79	D
LIST_S2	Benign	0.78	T;.
M_CAP	Benign	0.044	D
MetaRNN	Uncertain	0.52	D;D
MetaSVM	Benign	-0.67	T
MutationAssessor	Uncertain	2.4	M;M
PrimateAI	Benign	0.40	T
PROVEAN	Benign	-1.1	N;N
REVEL	Uncertain	0.38
Sift	Benign	0.054	T;T
Sift4G	Uncertain	0.057	T;T
Polyphen		1.0	D;D
Vest4		0.31
MutPred		0.60		Gain of sheet (P = 0.0827);Gain of sheet (P = 0.0827);
MVP		0.82
MPC		0.45
ClinPred		0.90	D
GERP RS		4.3
Varity_R		0.068
gMVP		0.21

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: chr1-117568289;