NM_015526.3:c.1205C>T

Variant names:

• chr19-36017970-G-A
• NM_015526.3:c.1205C>T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_015526.3(CLIP3):​c.1205C>T​(p.Ser402Phe) 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. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 31)
• Consequence: CLIP3 NM_015526.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 5.35

Genes affected

CLIP3 (HGNC:24314): (CAP-Gly domain containing linker protein 3) This gene encodes a member of the cytoplasmic linker protein 170 family. Members of this protein family contain a cytoskeleton-associated protein glycine-rich domain and mediate the interaction of microtubules with cellular organelles. The encoded protein plays a role in T cell apoptosis by facilitating the association of tubulin and the lipid raft ganglioside GD3. The encoded protein also functions as a scaffold protein mediating membrane localization of phosphorylated protein kinase B. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Dec 2010]

ENSG00000267698 (HGNC:):

ACMG classification

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=0.19272175).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLIP3	NM_015526.3	c.1205C>T	p.Ser402Phe	missense_variant	Exon 10 of 14	ENST00000360535.9	NP_056341.1
CLIP3	NM_001199570.2	c.1205C>T	p.Ser402Phe	missense_variant	Exon 9 of 13		NP_001186499.1
LOC101927572	NR_170987.1	n.234+1010G>A		intron_variant	Intron 2 of 3
LOC101927572	NR_170988.1	n.234+1010G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLIP3	ENST00000360535.9	c.1205C>T	p.Ser402Phe	missense_variant	Exon 10 of 14	1	NM_015526.3	ENSP00000353732.3
ENSG00000267698	ENST00000586962.1	n.228+1010G>A		intron_variant	Intron 2 of 3	1
CLIP3	ENST00000593074.5	c.1205C>T	p.Ser402Phe	missense_variant	Exon 9 of 13	2		ENSP00000466832.1
ENSG00000267698	ENST00000685157.1	n.243+1010G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 31

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Sep 12, 2024

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1205C>T (p.S402F) alteration is located in exon 9 (coding exon 9) of the CLIP3 gene. This alteration results from a C to T substitution at nucleotide position 1205, causing the serine (S) at amino acid position 402 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	Benign	0.11
BayesDel_addAF	Benign	-0.026	T
BayesDel_noAF	Benign	-0.28
CADD	Pathogenic	26
DANN	Uncertain	1.0
DEOGEN2	Benign	0.21	T;T
Eigen	Benign	-0.11
Eigen_PC	Benign	0.090
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Benign	0.78	.;T
M_CAP	Benign	0.024	T
MetaRNN	Benign	0.19	T;T
MetaSVM	Benign	-0.82	T
MutationAssessor	Benign	1.0	L;L
PrimateAI	Uncertain	0.51	T
PROVEAN	Benign	-2.2	N;.
REVEL	Benign	0.14
Sift	Uncertain	0.0070	D;.
Sift4G	Uncertain	0.0090	D;D
Polyphen		0.085	B;B
Vest4		0.51
MutPred		0.20		Loss of phosphorylation at S402 (P = 0.0047);Loss of phosphorylation at S402 (P = 0.0047);
MVP		0.49
MPC		0.84
ClinPred		0.85	D
GERP RS		4.5
Varity_R		0.14
gMVP		0.29

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		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: chr19-36508872;