Is CFAP44 p.Arg1495Trp (c.4483C>T) pathogenic?

CFAP44 p.Arg1495Trp (c.4483C>T) is classified Benign in CFAP44 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2019-12-31). AlphaMissense: ambiguous (0.4405); Low-frequency (popmax 2.23%, afr).

How common is CFAP44 p.Arg1495Trp (c.4483C>T) in the general population?

CFAP44 p.Arg1495Trp (c.4483C>T) is low-frequency (popmax 2.23%, afr) (gnomAD).

What do computational predictors say about CFAP44 p.Arg1495Trp (c.4483C>T)?

AlphaMissense predicts ambiguous (score 0.4405) — an in-silico prediction, not a clinical call.

CFAP44 p.Arg1495Trp

c.4483C>T · rs58191991 · VCV791437

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

ambiguous

0.4405 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 2.23%, afr)

Missense predictors

1/2 damaging

REVEL, SaProt · AlphaMissense no call

Computational evidence

Protein change
AlphaMissense	0.4405	ambiguous
REVEL	0.216	benign-leaning
SaProt	LLR -12.53	damaging
⇒ SaProt calls this damaging; REVEL does not; AlphaMissense makes no call.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>C here scores Δ0.33 · evaluated, not missing
Constraint at this position
Conservation	phyloP 3.7	GERP -3.1, phastCons 1
Regional constraint	o/e 0.93	unconstrained · MANE · 129 kb · p 0.0018 · regional, not allelic
Overall
CADD	23.2	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 2.23% African / African-American · 1,599/71,582 alleles

Filtering AF 2.14% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.11%

Overall 0.446% 6,756/1,515,284 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	2.23%	45
Middle Eastern	1.2%	83
Remaining individualsnot grpmax-eligible	0.515%	194
Admixed American	0.439%	228
European (non-Finnish)	0.38%	263
Ashkenazi Jewishnot grpmax-eligible	0.24%	416
Finnishnot grpmax-eligible	0.163%	615
South Asian	0.131%	765
East Asian	0.0148%	6,742

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.Arg1495Trp
Coding: c.4483C>T
MANE Select: NM_001164496
dbSNP: rs58191991
Type: single nucleotide variant
Location: chr3:113326478 (GRCh38)
Gene constraint: LOEUF 0.697 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 74.87 · 1 PDB
Residue 1495: a UniProt-annotated variant site (in spgf20)

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

Similar variants

CFAP44 p.Glu463Ter Pathogenic ★★ same type
CFAP44 c.4759-3C>T Benign ★★ same type
CFAP44 p.Ala157= Benign ★★ same type
CFAP44 p.Ala486Val Likely benign ★★ ⚠ same type
CFAP44 p.Arg1059Gln Benign ★★ same type
CFAP44 p.Arg1651Trp Benign/Likely benign ★★ ⚠ same type
CFAP44 p.Arg1806= Benign/Likely benign ★★ same type
CFAP44 p.Arg1845= Likely benign ★★ same type

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-arg1495trp (accessed [today's date]).

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