Classification
Category 4
curation
CMH MAF
184 /
13144 samples
(1.4%)
182 het.,
2 hom.
(98.9%)
186 /
26288 total alleles
(0.708%)
Genes
gene: PHYH
synonym(s): LN1, LNAP1, PAHX, PHYH1, RD, PHYH, ENSG00000107537
NM_001037537.1
[CDS]
hgvs_c: NM_001037537.1:c.434G>A
reference AA: R
variant AA: Q
reference codon: cGg
variant codon: cAg
cDNA pos: 927
CDS pos: 434
translation impact: non_synonymous
protein sequence:
NP_001032626.1
AA pos: 145
hgvs_p: NP_001032626.1:p.Arg145Gln
blosum: 1
SIFT: deleterious (0.01)
PolyPhen2: possibly_damaging (0.577)
NM_006214.3
[CDS]
Reportable
hgvs_c: NM_006214.3:c.734G>A
reference AA: R
variant AA: Q
reference codon: cGg
variant codon: cAg
cDNA pos: 822
CDS pos: 734
translation impact: non_synonymous
protein sequence:
NP_006205.1
AA pos: 245
hgvs_p: NP_006205.1:p.Arg245Gln
blosum: 1
SIFT: deleterious (0.01)
PolyPhen2: possibly_damaging (0.577)
dbSNP
rs62619919
GMAF = 0.005391
TOPMED_MAF = 0.00462697502548419
ClinVar
198539
clinvar_significance = Conflicting_interpretations_of_pathogenicity
clinvar_disease = Nonsyndromic cleft lip palate
clinvar_disease = Phytanic acid storage disease
Exome Variant Server
EVS
EVS MAF (European American/African American/All) = 0.006395,0.000908,0.004536
ExAC
ExAC
| Ethnicity |
Count / Number |
MAF |
| African |
12 / 10406 |
0.115% |
| America/Latino |
24 / 11578 |
0.207% |
| East Asian |
2 / 8654 |
0.0231% |
| Finnish |
164 / 6614 |
2.48% |
| Non-Finnish |
530 / 66740 |
0.794% |
| Other |
11 / 908 |
1.21% |
| South Asian |
209 / 16512 |
1.27% |
| Total MAF |
952 / 121412 |
0.784% |
COSMIC
COSMIC Mutation ID = COSV99036280
COSMIC_FATHMM_PREDICTION = PATHOGENIC
COSMIC_MUTATION_SOMATIC_STATUS = false
gnomAD
gnomAD
Source: Genome / Exome
| Ethnicity |
Count / Number |
MAF |
| African |
26 / 24960 |
0.104% |
| America/Latino |
73 / 35438 |
0.206% |
| Ashkenazi Jewish |
21 / 10370 |
0.203% |
| East Asian |
2 / 19952 |
0.01% |
| Finnish |
634 / 25120 |
2.52% |
| Non-Finnish |
995 / 129188 |
0.77% |
| Other |
46 / 7224 |
0.637% |
| South Asian |
389 / 30616 |
1.27% |
| Korean |
1 / 3818 |
0.0262% |
| Japanese |
0 / 152 |
0% |
| Other East Asian |
1 / 14424 |
0.00693% |
| Bulgarian |
31 / 2670 |
1.16% |
| Estonian |
72 / 4822 |
1.49% |
| North-Western European |
315 / 50816 |
0.62% |
| Southern European |
121 / 11610 |
1.04% |
| Swedish |
186 / 26134 |
0.712% |
| Other non-Finnish European |
270 / 33136 |
0.815% |
| Total MAF |
2186 / 282868 |
0.773% |
curated_classification = 4
Export Variant