rs762760856
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PP3_StrongPP5
The NM_001164496.2(CFAP44):c.1769T>A(p.Leu590Gln) 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). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L590V) has been classified as Likely benign.
Frequency
Consequence
NM_001164496.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CFAP44 | NM_001164496.2 | c.1769T>A | p.Leu590Gln | missense_variant | 14/35 | ENST00000393845.9 | |
LOC127898559 | NR_183046.1 | n.4850+3378T>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CFAP44 | ENST00000393845.9 | c.1769T>A | p.Leu590Gln | missense_variant | 14/35 | 5 | NM_001164496.2 | P2 | |
CFAP44 | ENST00000295868.6 | c.1769T>A | p.Leu590Gln | missense_variant | 14/21 | 1 | A2 | ||
CFAP44 | ENST00000475568.1 | n.387T>A | non_coding_transcript_exon_variant | 2/4 | 4 | ||||
CFAP44 | ENST00000488854.6 | c.*1185T>A | 3_prime_UTR_variant, NMD_transcript_variant | 11/16 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251098Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135720
GnomAD4 exome Cov.: 31
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Spermatogenic failure 20 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Dec 23, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at