14-57231660-T-G

Variant names:

• chr14-57231660-T-G
• rs752054409
• NM_006544.4:c.994A>C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BS2

The NM_006544.4(EXOC5):​c.994A>C​(p.Thr332Pro) variant causes a missense change. The variant allele was found at a frequency of 0.00000342 in 1,461,054 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000034 (1 hom.)
• Consequence: EXOC5 NM_006544.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.82

Genes affected

EXOC5 (HGNC:10696): (exocyst complex component 5) The protein encoded by this gene is a component of the exocyst complex, a multiple protein complex essential for targeting exocytic vesicles to specific docking sites on the plasma membrane. Though best characterized in yeast, the component proteins and functions of exocyst complex have been demonstrated to be highly conserved in higher eukaryotes. At least eight components of the exocyst complex, including this protein, are found to interact with the actin cytoskeletal remodeling and vesicle transport machinery. The complex is also essential for the biogenesis of epithelial cell surface polarity. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BS2: High AC in GnomAdExome4 at 5 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EXOC5	NM_006544.4	c.994A>C	p.Thr332Pro	missense_variant	Exon 11 of 18	ENST00000621441.5	NP_006535.1
EXOC5	XM_005267272.4	c.1108A>C	p.Thr370Pro	missense_variant	Exon 11 of 18		XP_005267329.1
EXOC5	XM_047430882.1	c.829A>C	p.Thr277Pro	missense_variant	Exon 11 of 18		XP_047286838.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EXOC5	ENST00000621441.5	c.994A>C	p.Thr332Pro	missense_variant	Exon 11 of 18	1	NM_006544.4	ENSP00000484855.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000342 AC: 5 AN: 1461054 Hom.: 1 Cov.: 30 AF XY: 0.00000688 AC XY: 5 AN XY: 726822

Gnomad4 AFR exome AF: 0.000149

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: 0.00

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	0.24
BayesDel_addAF	Pathogenic	0.21	D
BayesDel_noAF	Uncertain	0.070
CADD	Pathogenic	27
DANN	Uncertain	1.0
DEOGEN2	Benign	0.057	T;T;T
Eigen	Uncertain	0.52
Eigen_PC	Uncertain	0.57
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.95	D;D;D
M_CAP	Benign	0.018	T
MetaRNN	Uncertain	0.63	D;D;D
MetaSVM	Benign	-0.94	T
MutationAssessor	Benign	1.6	L;.;.
PrimateAI	Uncertain	0.69	T
PROVEAN	Benign	-0.90	.;N;N
REVEL	Uncertain	0.33
Sift	Benign	0.053	.;T;T
Sift4G	Benign	0.062	T;T;D
Polyphen		1.0	D;.;D
Vest4		0.67
MutPred		0.54		Loss of phosphorylation at T332 (P = 0.0631);Loss of phosphorylation at T332 (P = 0.0631);.;
MVP		0.67
MPC		0.97
ClinPred		0.85	D
GERP RS		5.6
Varity_R		0.51
gMVP		0.73

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

LitVar

Other links and lift over

dbSNP: rs752054409; hg19: chr14-57698378;