chr14-67473460-C-T

Variant names:

• chr14-67473460-C-T
• NM_001348543.2:c.464G>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001348543.2(TMEM229B):​c.464G>A​(p.Gly155Asp) 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. 16/21 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: TMEM229B NM_001348543.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.0390
• Publications: 0 publications found

Genes affected

TMEM229B (HGNC:20130): (transmembrane protein 229B) Predicted to act upstream of or within response to bacterium. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

GPHN (HGNC:15465): (gephyrin) This gene encodes a neuronal assembly protein that anchors inhibitory neurotransmitter receptors to the postsynaptic cytoskeleton via high affinity binding to a receptor subunit domain and tubulin dimers. In nonneuronal tissues, the encoded protein is also required for molybdenum cofactor biosynthesis. Mutations in this gene may be associated with the neurological condition hyperplexia and also lead to molybdenum cofactor deficiency. Numerous alternatively spliced transcript variants encoding different isoforms have been described; however, the full-length nature of all transcript variants is not currently known. [provided by RefSeq, Jul 2008]

GPHN Gene-Disease associations (from GenCC):

• sulfite oxidase deficiency due to molybdenum cofactor deficiency type C

  Inheritance: AR Classification: STRONG, MODERATE, LIMITED Submitted by: G2P, ClinGen, Labcorp Genetics (formerly Invitae), Ambry Genetics
• hereditary hyperekplexia

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• complex neurodevelopmental disorder

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.034963697).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001348543.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM229B	NM_001348543.2	MANE Select	c.464G>A	p.Gly155Asp	missense	Exon 3 of 3	NP_001335472.1	Q8NBD8
	TMEM229B	NM_001348541.2		c.596G>A	p.Gly199Asp	missense	Exon 3 of 3	NP_001335470.1
	TMEM229B	NM_001348542.2		c.464G>A	p.Gly155Asp	missense	Exon 3 of 3	NP_001335471.1	Q8NBD8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM229B	ENST00000554480.6	TSL:2 MANE Select	c.464G>A	p.Gly155Asp	missense	Exon 3 of 3	ENSP00000450859.2	Q8NBD8
	TMEM229B	ENST00000357461.7	TSL:2	c.464G>A	p.Gly155Asp	missense	Exon 3 of 3	ENSP00000350050.2	Q8NBD8
	TMEM229B	ENST00000554278.6	TSL:4	c.464G>A	p.Gly155Asp	missense	Exon 3 of 3	ENSP00000452402.2	Q8NBD8

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.077
BayesDel_addAF	Benign	-0.29	T
BayesDel_noAF	Benign	-0.66
CADD	Benign	9.8
DANN	Benign	0.97
DEOGEN2	Benign	0.019	T
Eigen	Benign	-0.97
Eigen_PC	Benign	-0.90
FATHMM_MKL	Benign	0.093	N
LIST_S2	Benign	0.57	T
M_CAP	Benign	0.0046	T
MetaRNN	Benign	0.035	T
MetaSVM	Benign	-0.98	T
MutationAssessor	Benign	0.0	N
PhyloP100		0.039
PrimateAI	Benign	0.35	T
PROVEAN	Benign	0.37	N
REVEL	Benign	0.039
Sift	Benign	0.69	T
Sift4G	Benign	0.72	T
Polyphen		0.0030	B
Vest4		0.056
MutPred		0.18		Loss of glycosylation at S154 (P = 0.0428)
MVP		0.014
MPC		1.1
ClinPred		0.081	T
GERP RS		2.5
Varity_R		0.038
gMVP		0.76
Mutation Taster		=93/7	polymorphism

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

Other links and lift over

hg19: chr14-67940177; COSMIC: COSV107426143; COSMIC: COSV107426143;