rs797045181

Variant summary

Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PP3_StrongPP5

The NM_207352.4(CYP4V2):​c.1396A>G​(p.Asn466Asp) variant causes a missense change involving the alteration of a conserved nucleotide. 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).

Frequency

Genomes: not found (cov: 32)

Consequence

CYP4V2
NM_207352.4 missense

Scores

11
6
2

Clinical Significance

Pathogenic no assertion criteria provided P:1

Conservation

PhyloP100: 8.35
Variant links:
Genes affected
CYP4V2 (HGNC:23198): (cytochrome P450 family 4 subfamily V member 2) This gene encodes a member of the cytochrome P450 hemethiolate protein superfamily which are involved in oxidizing various substrates in the metabolic pathway. It is implicated in the metabolism of fatty acid precursors into n-3 polyunsaturated fatty acids. Mutations in this gene result in Bietti crystalline corneoretinal dystrophy. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

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, 0.984
PP5
Variant 4-186209263-A-G is Pathogenic according to our data. Variant chr4-186209263-A-G is described in ClinVar as [Pathogenic]. Clinvar id is 209986.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CYP4V2NM_207352.4 linkuse as main transcriptc.1396A>G p.Asn466Asp missense_variant 10/11 ENST00000378802.5
CYP4V2XM_005262935.5 linkuse as main transcriptc.1393A>G p.Asn465Asp missense_variant 10/11
CYP4V2XM_047450077.1 linkuse as main transcriptc.1000A>G p.Asn334Asp missense_variant 8/9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CYP4V2ENST00000378802.5 linkuse as main transcriptc.1396A>G p.Asn466Asp missense_variant 10/111 NM_207352.4 P1Q6ZWL3-1
CYP4V2ENST00000502665.1 linkuse as main transcriptn.631A>G non_coding_transcript_exon_variant 4/51
CYP4V2ENST00000507209.5 linkuse as main transcriptn.6094A>G non_coding_transcript_exon_variant 5/61
CYP4V2ENST00000513354.5 linkuse as main transcriptn.486A>G non_coding_transcript_exon_variant 4/51

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
36
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Bietti crystalline corneoretinal dystrophy Pathogenic:1
Pathogenic, no assertion criteria providedliterature onlyOMIMJun 14, 2013- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.98
BayesDel_addAF
Uncertain
0.12
D
BayesDel_noAF
Uncertain
-0.060
CADD
Pathogenic
28
DANN
Uncertain
1.0
DEOGEN2
Benign
0.32
T
Eigen
Pathogenic
0.92
Eigen_PC
Pathogenic
0.86
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Pathogenic
0.98
D
M_CAP
Uncertain
0.28
D
MetaRNN
Pathogenic
0.98
D
MetaSVM
Uncertain
0.43
D
MutationAssessor
Pathogenic
4.1
H
MutationTaster
Benign
1.0
D
PrimateAI
Uncertain
0.78
T
PROVEAN
Pathogenic
-4.8
D
REVEL
Pathogenic
0.79
Sift
Pathogenic
0.0
D
Sift4G
Pathogenic
0.0
D
Polyphen
1.0
D
Vest4
0.93
MutPred
0.94
Loss of glycosylation at S461 (P = 0.0416);
MVP
0.96
MPC
0.43
ClinPred
1.0
D
GERP RS
5.4
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.95
gMVP
0.87

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs797045181; hg19: chr4-187130417; API