chr18-36355575-G-T

Variant names:

• chr18-36355575-G-T
• NM_001281740.3:c.202G>T

Variant summary

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

The NM_001281740.3(FHOD3):​c.202G>T​(p.Ala68Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: FHOD3 NM_001281740.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.26

Genes affected

FHOD3 (HGNC:26178): (formin homology 2 domain containing 3) The protein encoded by this gene is a member of the diaphanous-related formins (DRF), and contains multiple domains, including GBD (GTPase-binding domain), DID (diaphanous inhibitory domain), FH1 (formin homology 1), FH2 (formin homology 2), and DAD (diaphanous auto-regulatory domain) domains. This protein is thought to play a role in actin filament polymerization in cardiomyocytes. Mutations in this gene have been associated with dilated cardiomyopathy (DCM), characterized by dilation of the ventricular chamber, leading to impairment of systolic pump function and subsequent heart failure. Increased levels of the protein encoded by this gene have been observed in individuals with hypertrophic cardiomyopathy (HCM). Alternative splicing results in multiple transcript variants encoding different isoforms. A muscle-specific isoform has been shown to possess a casein kinase 2 (CK2) phosphorylation site at the C-terminal end of the FH2 domain. Phosphorylation of this site alters its interaction with sequestosome 1 (SQSTM1), and targets this isoform to myofibrils, while other isoforms form cytoplasmic aggregates. [provided by RefSeq, Aug 2015]

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=0.09117696).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FHOD3	NM_001281740.3	c.202G>T	p.Ala68Ser	missense_variant	Exon 2 of 29	ENST00000590592.6	NP_001268669.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FHOD3	ENST00000590592.6	c.202G>T	p.Ala68Ser	missense_variant	Exon 2 of 29	1	NM_001281740.3	ENSP00000466937.1
FHOD3	ENST00000257209.8	c.202G>T	p.Ala68Ser	missense_variant	Exon 2 of 25	1		ENSP00000257209.3
FHOD3	ENST00000359247.8	c.202G>T	p.Ala68Ser	missense_variant	Exon 2 of 24	1		ENSP00000352186.3
FHOD3	ENST00000589114.5	n.321G>T		non_coding_transcript_exon_variant	Exon 2 of 14	2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.068
BayesDel_addAF	Benign	-0.26	T
BayesDel_noAF	Benign	-0.61
CADD	Benign	15
DANN	Benign	0.91
DEOGEN2	Benign	0.0054	.;.;T
Eigen	Benign	-0.91
Eigen_PC	Benign	-0.72
FATHMM_MKL	Benign	0.75	D
LIST_S2	Benign	0.79	T;T;T
M_CAP	Benign	0.0046	T
MetaRNN	Benign	0.091	T;T;T
MetaSVM	Benign	-0.96	T
MutationAssessor	Benign	-1.8	N;N;N
PrimateAI	Benign	0.36	T
PROVEAN	Benign	0.090	N;.;N
REVEL	Benign	0.039
Sift	Benign	0.58	T;.;T
Sift4G	Benign	0.42	T;T;T
Polyphen		0.0040	B;.;B
Vest4		0.29
MutPred		0.22		Gain of disorder (P = 0.0399);Gain of disorder (P = 0.0399);Gain of disorder (P = 0.0399);
MVP		0.043
MPC		0.15
ClinPred		0.39	T
GERP RS		-0.77
Varity_R		0.048
gMVP		0.084

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: chr18-33935538;