NM_015166.4:c.1031A>C

Variant names:

• chr22-50064062-T-G
• rs11568188
• NM_015166.4:c.1031A>C

Variant summary

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

The NM_015166.4(MLC1):​c.1031A>C​(p.Asn344Thr) 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. 16/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N344S) has been classified as Benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MLC1 NM_015166.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.631
• Publications: 0 publications found

Genes affected

MLC1 (HGNC:17082): (modulator of VRAC current 1) The function of this gene product is unknown; however, homology to other proteins suggests that it may be an integral membrane transporter. Mutations in this gene have been associated with megalencephalic leukoencephalopathy with subcortical cysts, an autosomal recessive neurological disorder. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

MLC1 Gene-Disease associations (from GenCC):

• megalencephalic leukoencephalopathy with subcortical cysts 1

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P, Myriad Women’s Health
• megalencephalic leukoencephalopathy with subcortical cysts

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

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=0.031273037).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015166.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MLC1	NM_015166.4	MANE Select	c.1031A>C	p.Asn344Thr	missense	Exon 11 of 12	NP_055981.1
	MLC1	NM_001376472.1		c.1031A>C	p.Asn344Thr	missense	Exon 10 of 11	NP_001363401.1
	MLC1	NM_001376473.1		c.1031A>C	p.Asn344Thr	missense	Exon 12 of 13	NP_001363402.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MLC1	ENST00000311597.10	TSL:1 MANE Select	c.1031A>C	p.Asn344Thr	missense	Exon 11 of 12	ENSP00000310375.6
	MLC1	ENST00000395876.6	TSL:1	c.1031A>C	p.Asn344Thr	missense	Exon 11 of 12	ENSP00000379216.2
	MLC1	ENST00000483836.1	TSL:2	n.388A>C		non_coding_transcript_exon	Exon 4 of 5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 37

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.057
BayesDel_addAF	Benign	-0.19	T
BayesDel_noAF	Benign	-0.51
CADD	Benign	6.4
DANN	Benign	0.41
DEOGEN2	Benign	0.018	T
Eigen	Benign	-1.6
Eigen_PC	Benign	-1.5
FATHMM_MKL	Benign	0.00016	N
LIST_S2	Benign	0.077	T
M_CAP	Benign	0.045	D
MetaRNN	Benign	0.031	T
MetaSVM	Benign	-0.76	T
MutationAssessor	Benign	-1.1	N
PhyloP100		0.63
PrimateAI	Uncertain	0.59	T
PROVEAN	Benign	1.6	N
REVEL	Benign	0.19
Sift	Benign	0.65	T
Sift4G	Benign	0.61	T
Polyphen		0.0	B
Vest4		0.13
MutPred		0.16		Gain of phosphorylation at N344 (P = 0.1445)
MVP		0.52
MPC		0.25
ClinPred		0.037	T
GERP RS		1.7
Varity_R		0.036
gMVP		0.084
Mutation Taster		=98/2	polymorphism

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

Other links and lift over

dbSNP: rs11568188; hg19: chr22-50502491;