Is CFAP44 p.Gln87Leu (c.260A>T) pathogenic?

CFAP44 p.Gln87Leu (c.260A>T) is classified Benign in CFAP44 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2019-12-31). AlphaMissense: likely benign (0.0839); Low-frequency (popmax 1.69%, afr).

How common is CFAP44 p.Gln87Leu (c.260A>T) in the general population?

CFAP44 p.Gln87Leu (c.260A>T) is low-frequency (popmax 1.69%, afr) (gnomAD).

What do computational predictors say about CFAP44 p.Gln87Leu (c.260A>T)?

AlphaMissense predicts likely benign (score 0.0839) — an in-silico prediction, not a clinical call.

CFAP44 p.Gln87Leu

c.260A>T · rs115750112 · VCV720916

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.0839 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 1.69%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0839	likely benign
REVEL	0.052	moderately benign-leaning
SaProt	LLR -5.11	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 -2.9	GERP -4.9
Regional constraint	o/e 1.05	unconstrained · MANE · 7,513 bp · p 0.55 · regional, not allelic
Overall
CADD	1.554	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 1.69% African / African-American · 1,265/74,886 alleles

Filtering AF 1.61% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.58%

Overall 0.0897% 1,447/1,612,978 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	1.69%	59
Middle Eastern	0.165%	605
Remaining individualsnot grpmax-eligible	0.128%	780
Admixed American	0.116%	865
South Asian	0.0055%	18,188
European (non-Finnish)	0.00153%	65,538

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.Gln87Leu
Coding: c.260A>T
MANE Select: NM_001164496
dbSNP: rs115750112
Type: single nucleotide variant
Location: chr3:113426271 (GRCh38)
Gene constraint: LOEUF 0.697 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 74.87 · 1 PDB
Residue 87: the 'disordered' region

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

Similar variants

CFAP44 p.Gln87Ter Pathogenic ★ same residue
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.Arg1495Trp Benign ★★ ⚠ same type
CFAP44 p.Arg1651Trp Benign/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-gln87leu (accessed [today's date]).

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