NM_024769.5:c.1082G>C

Variant summary

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

The NM_024769.5(CLMP):​c.1082G>C​(p.Ser361Thr) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)

Consequence

CLMP
NM_024769.5 missense

Scores

1
18

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.62
Variant links:
Genes affected
CLMP (HGNC:24039): (CXADR like membrane protein) This gene encodes a type I transmembrane protein that is localized to junctional complexes between endothelial and epithelial cells and may have a role in cell-cell adhesion. Expression of this gene in white adipose tissue is implicated in adipocyte maturation and development of obesity. This gene is also essential for normal intestinal development and mutations in the gene are associated with congenital short bowel syndrome. [provided by RefSeq, Aug 2015]

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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=0.14916763).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CLMPNM_024769.5 linkc.1082G>C p.Ser361Thr missense_variant Exon 7 of 7 ENST00000448775.4 NP_079045.1 Q9H6B4B4E3S3
LOC124902775XR_007062927.1 linkn.871-9500C>G intron_variant Intron 1 of 1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CLMPENST00000448775.4 linkc.1082G>C p.Ser361Thr missense_variant Exon 7 of 7 1 NM_024769.5 ENSP00000405577.2 Q9H6B4
CLMPENST00000530371.5 linkn.556G>C non_coding_transcript_exon_variant Exon 4 of 4 4
ENSG00000288061ENST00000660892.2 linkn.226+10001C>G intron_variant Intron 2 of 2
CLMPENST00000527977.5 linkn.*192G>C downstream_gene_variant 3

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
33

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Inborn genetic diseases Uncertain:1
Dec 23, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.1082G>C (p.S361T) alteration is located in exon 7 (coding exon 7) of the CLMP gene. This alteration results from a G to C substitution at nucleotide position 1082, causing the serine (S) at amino acid position 361 to be replaced by a threonine (T). 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
0.069
BayesDel_addAF
Benign
-0.19
T
BayesDel_noAF
Benign
-0.51
CADD
Benign
17
DANN
Benign
0.71
DEOGEN2
Benign
0.0034
T
Eigen
Benign
0.066
Eigen_PC
Benign
0.21
FATHMM_MKL
Uncertain
0.88
D
LIST_S2
Benign
0.63
T
M_CAP
Benign
0.017
T
MetaRNN
Benign
0.15
T
MetaSVM
Benign
-0.65
T
MutationAssessor
Benign
1.8
L
PrimateAI
Benign
0.35
T
PROVEAN
Benign
0.52
N
REVEL
Benign
0.22
Sift
Benign
0.58
T
Sift4G
Benign
0.86
T
Polyphen
0.12
B
Vest4
0.079
MutPred
0.25
Gain of glycosylation at S361 (P = 0.0211);
MVP
0.64
MPC
0.29
ClinPred
0.41
T
GERP RS
5.4
Varity_R
0.079
gMVP
0.39

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: chr11-122944222; API