rs1411193128

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_032439.4(PHYHIPL):​c.784C>A​(p.Pro262Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,828 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. P262S) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 31)
Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

PHYHIPL
NM_032439.4 missense

Scores

4
10
5

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.75
Variant links:
Genes affected
PHYHIPL (HGNC:29378): (phytanoyl-CoA 2-hydroxylase interacting protein like) Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PHYHIPLNM_032439.4 linkc.784C>A p.Pro262Thr missense_variant Exon 5 of 5 ENST00000373880.9 NP_115815.2 Q96FC7-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PHYHIPLENST00000373880.9 linkc.784C>A p.Pro262Thr missense_variant Exon 5 of 5 1 NM_032439.4 ENSP00000362987.4 Q96FC7-1
PHYHIPLENST00000373878.3 linkc.706C>A p.Pro236Thr missense_variant Exon 5 of 5 1 ENSP00000362985.3 Q96FC7-2
PHYHIPLENST00000486074.2 linkn.*725C>A non_coding_transcript_exon_variant Exon 6 of 6 2 ENSP00000423634.1 Q96FC7-3
PHYHIPLENST00000486074.2 linkn.*725C>A 3_prime_UTR_variant Exon 6 of 6 2 ENSP00000423634.1 Q96FC7-3

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461828
Hom.:
0
Cov.:
30
AF XY:
0.00000138
AC XY:
1
AN XY:
727222
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.0000166
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.085
BayesDel_addAF
Pathogenic
0.19
D
BayesDel_noAF
Uncertain
0.030
CADD
Benign
23
DANN
Uncertain
1.0
DEOGEN2
Benign
0.30
T;.
Eigen
Uncertain
0.64
Eigen_PC
Pathogenic
0.70
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Uncertain
0.92
D;D
M_CAP
Benign
0.054
D
MetaRNN
Uncertain
0.47
T;T
MetaSVM
Benign
-0.86
T
MutationAssessor
Uncertain
2.3
M;.
PrimateAI
Uncertain
0.76
T
PROVEAN
Pathogenic
-4.7
D;D
REVEL
Uncertain
0.41
Sift
Uncertain
0.0020
D;D
Sift4G
Uncertain
0.047
D;D
Polyphen
0.70
P;P
Vest4
0.69
MutPred
0.53
Gain of relative solvent accessibility (P = 0.0479);.;
MVP
0.49
MPC
0.94
ClinPred
0.96
D
GERP RS
5.8
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.6
Varity_R
0.59
gMVP
0.31

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: chr10-61005004; API