Is CFAP44 p.Ala486Val (c.1457C>T) pathogenic?

CFAP44 p.Ala486Val (c.1457C>T) is classified Likely benign in CFAP44 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2019-12-31). AlphaMissense: likely benign (0.1337); Rare (popmax 0.34%, afr).

How common is CFAP44 p.Ala486Val (c.1457C>T) in the general population?

CFAP44 p.Ala486Val (c.1457C>T) is rare (popmax 0.34%, afr) (gnomAD).

What do computational predictors say about CFAP44 p.Ala486Val (c.1457C>T)?

AlphaMissense predicts likely benign (score 0.1337) — an in-silico prediction, not a clinical call.

CFAP44 p.Ala486Val

c.1457C>T · rs75322072 · VCV790540

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1337 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.34%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1337	likely benign
REVEL	0.196	benign-leaning
SaProt	LLR -9.30	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 3.9	GERP 0.38, phastCons 1
Regional constraint	o/e 0.93	unconstrained · MANE · 129 kb · p 0.0018 · regional, not allelic
Overall
CADD	21.4	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 0.34% African / African-American · 253/74,506 alleles

Filtering AF 0.305% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.292%

Overall 0.0482% 774/1,606,382 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.34%	294
Middle Eastern	0.266%	376
Admixed American	0.19%	526
Remaining individualsnot grpmax-eligible	0.113%	887
European (non-Finnish)	0.0273%	3,665
Ashkenazi Jewishnot grpmax-eligible	0.00682%	14,658

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.Ala486Val
Coding: c.1457C>T
MANE Select: NM_001164496
dbSNP: rs75322072
Type: single nucleotide variant
Location: chr3:113400562 (GRCh38)
Gene constraint: LOEUF 0.697 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 74.87 · 1 PDB
Residue 486: 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.Arg1059Gln Benign ★★ same type
CFAP44 p.Arg1495Trp 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-ala486val (accessed [today's date]).

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