rs2279381

Variant names:

• chr6-122780399-C-A
• NM_001446.5:c.182C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-122780399-C-A
• chr6-122780399-C-G
• chr6-122780399-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2 PP3_Moderate

The NM_001446.5(FABP7):​c.182C>A​(p.Thr61Lys) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic 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. T61M) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: FABP7 NM_001446.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.92

Genes affected

FABP7 (HGNC:3562): (fatty acid binding protein 7) The gene encodes a small, highly conserved cytoplasmic protein that bind long-chain fatty acids and other hydrophobic ligands. The encoded protein is important in the establishment of the radial glial fiber in the developing brain. Alternative splicing and promoter usage results in multiple transcript variants encoding different isoforms. Pseudogenes of this gene are found on multiple chromosomes. [provided by RefSeq, Jan 2016]

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.863

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FABP7	NM_001446.5	c.182C>A	p.Thr61Lys	missense_variant	Exon 2 of 4	ENST00000368444.8	NP_001437.1
FABP7	NM_001319039.2	c.182C>A	p.Thr61Lys	missense_variant	Exon 2 of 3		NP_001305968.1
FABP7	NM_001319042.2	c.170C>A	p.Thr57Lys	missense_variant	Exon 2 of 4		NP_001305971.1
FABP7	NM_001319041.2	c.182C>A	p.Thr61Lys	missense_variant	Exon 2 of 2		NP_001305970.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FABP7	ENST00000368444.8	c.182C>A	p.Thr61Lys	missense_variant	Exon 2 of 4	1	NM_001446.5	ENSP00000357429.3
FABP7	ENST00000356535.4	c.182C>A	p.Thr61Lys	missense_variant	Exon 2 of 3	1		ENSP00000348931.4

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.73
BayesDel_addAF	Uncertain	0.13	D
BayesDel_noAF	Uncertain	-0.050
CADD	Uncertain	24
DANN	Uncertain	0.99
DEOGEN2	Benign	0.26	T;.
Eigen	Uncertain	0.64
Eigen_PC	Uncertain	0.56
FATHMM_MKL	Uncertain	0.94	D
LIST_S2	Benign	0.61	T;T
M_CAP	Benign	0.052	D
MetaRNN	Pathogenic	0.86	D;D
MetaSVM	Benign	-1.0	T
MutationAssessor	Uncertain	2.4	M;M
PrimateAI	Uncertain	0.71	T
PROVEAN	Pathogenic	-5.0	D;D
REVEL	Uncertain	0.30
Sift	Uncertain	0.017	D;D
Sift4G	Uncertain	0.025	D;D
Polyphen		1.0	D;.
Vest4		0.79
MutPred		0.55		Gain of ubiquitination at T61 (P = 0.0219);Gain of ubiquitination at T61 (P = 0.0219);
MVP		0.67
MPC		0.71
ClinPred		0.99	D
GERP RS		3.6
Varity_R		0.89
gMVP		0.81

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: chr6-123101544;