Is CFAP44 p.Met508Ile (c.1524G>A) pathogenic?

CFAP44 p.Met508Ile (c.1524G>A) is classified Conflicting classifications of pathogenicity in CFAP44 (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2021-10-27). AlphaMissense: likely benign (0.1666); Rare (popmax 0.39%, afr); Associated with Inborn genetic diseases.

What condition is associated with CFAP44 p.Met508Ile (c.1524G>A)?

CFAP44 p.Met508Ile (c.1524G>A) is associated with Inborn genetic diseases (ClinVar).

How common is CFAP44 p.Met508Ile (c.1524G>A) in the general population?

CFAP44 p.Met508Ile (c.1524G>A) is rare (popmax 0.39%, afr) (gnomAD).

What do computational predictors say about CFAP44 p.Met508Ile (c.1524G>A)?

AlphaMissense predicts likely benign (score 0.1666) — an in-silico prediction, not a clinical call.

CFAP44 p.Met508Ile

c.1524G>A · rs140307657 · VCV760210

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1666 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.39%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1666	likely benign
REVEL	0.052	moderately benign-leaning
SaProt	LLR -5.00	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.7	GERP 1.1, phastCons 1
Regional constraint	o/e 0.93	unconstrained · MANE · 129 kb · p 0.0018 · regional, not allelic
Overall
CADD	16.59	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.39% African / African-American · 291/74,678 alleles

Filtering AF 0.353% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.338%

Overall 0.0208% 333/1,603,326 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.39%	257
Admixed American	0.0326%	3,065
Remaining individualsnot grpmax-eligible	0.0274%	3,646
European (non-Finnish)	0.00051%	195,925

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: CFAP44
Protein: p.Met508Ile
Coding: c.1524G>A
MANE Select: NM_001164496
dbSNP: rs140307657
Type: single nucleotide variant
Location: chr3:113399951 (GRCh38)
Gene constraint: LOEUF 0.697 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 74.87 · 1 PDB
Residue 508: a UniProt-annotated variant site (in spgf20)

Full CFAP44 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CFAP44 p.Ala161Gly Uncertain significance ★ ⚠ same condition
CFAP44 p.Ala712Val Uncertain significance ★ ⚠ same condition
CFAP44 p.Arg495Gln Uncertain significance ★ ⚠ same condition
CFAP44 p.Arg522Gln Uncertain significance ★ ⚠ same condition
CFAP44 p.Arg557Gln Uncertain significance ★ ⚠ same condition
CFAP44 p.Arg585Cys Uncertain significance ★ ⚠ same condition
CFAP44 p.Arg606Met Uncertain significance ★ ⚠ same condition
CFAP44 p.Arg703Met Uncertain significance ★ ⚠ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/cfap44-p-met508ile (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown