rs121908190

chr11-119345516-A-Gchr11-119345516-A-T

Variant summary

Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2 PP3_Strong PP5

The NM_031433.4(MFRP):c.545T>C(p.Ile182Thr) 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. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I182M) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MFRP NM_031433.4 missense
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 4.94

Genes affected

MFRP (HGNC:18121): (membrane frizzled-related protein) This gene encodes a member of the frizzled-related protein family. The encoded protein plays an important role in eye development and mutations in this gene have been associated with nanophthalmos, posterior microphthalmia, retinitis pigmentosa, foveoschisis, and optic disc drusen. The protein is encoded by a bicistronic transcript which also encodes C1q and tumor necrosis factor related protein 5 (C1QTNF5). [provided by RefSeq, Jun 2013]

C1QTNF5 (HGNC:):

ACMG classification

Verdict is Likely_pathogenic. Variant got 7 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.982
• PP5: Variant 11-119345516-A-G is Pathogenic according to our data. Variant chr11-119345516-A-G is described in ClinVar as [Pathogenic]. Clinvar id is 4477.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr11-119345516-A-G is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MFRP	NM_031433.4	c.545T>C	p.Ile182Thr	missense_variant	5/15	ENST00000619721.6
C1QTNF5	NM_015645.5	c.-2092T>C		5_prime_UTR_variant	5/15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MFRP	ENST00000619721.6	c.545T>C	p.Ile182Thr	missense_variant	5/15	1	NM_031433.4	P1
MFRP	ENST00000360167.4	c.545T>C	p.Ile182Thr	missense_variant	5/10	2
MFRP	ENST00000529147.2	n.508T>C		non_coding_transcript_exon_variant	4/6	5
MFRP	ENST00000634542.1	c.*136T>C		3_prime_UTR_variant, NMD_transcript_variant	4/5	3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

Alfa AF: 0.00418 Hom.: 1

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Nanophthalmos 2 Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Jul 05, 2005

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.96
BayesDel_addAF	Pathogenic	0.24	D
BayesDel_noAF	Uncertain	0.10
Cadd	Uncertain	24
Dann	Uncertain	1.0
DEOGEN2	Benign	0.38	T;.
Eigen	Uncertain	0.51
Eigen_PC	Uncertain	0.38
FATHMM_MKL	Uncertain	0.79	D
LIST_S2	Benign	0.77	T;T
M_CAP	Benign	0.047	D
MetaRNN	Pathogenic	0.98	D;D
MetaSVM	Uncertain	-0.16	T
MutationAssessor	Pathogenic	3.9	H;H
MutationTaster	Benign	0.78	A;A;A;A
PrimateAI	Benign	0.42	T
Sift4G	Uncertain	0.0090	D;D
Polyphen		0.86	P;.
Vest4		0.82
MutPred		0.93		Loss of stability (P = 0.039);Loss of stability (P = 0.039);
MVP		0.40
ClinPred		0.98	D
GERP RS		4.0
Varity_R		0.42
gMVP		0.73

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

Publications

LitVar

Other links and lift over

dbSNP: rs121908190; hg19: chr11-119216226;