Is CFAP44 p.Phe1795Ser (c.5384T>C) pathogenic?

CFAP44 p.Phe1795Ser (c.5384T>C) is classified Uncertain significance in CFAP44 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-03-12). AlphaMissense: likely pathogenic (0.6069); Ultra-rare (popmax 0.0214%, nfe); Associated with CFAP44-related disorder.

What condition is associated with CFAP44 p.Phe1795Ser (c.5384T>C)?

CFAP44 p.Phe1795Ser (c.5384T>C) is associated with CFAP44-related disorder (ClinVar).

How common is CFAP44 p.Phe1795Ser (c.5384T>C) in the general population?

CFAP44 p.Phe1795Ser (c.5384T>C) is ultra-rare (popmax 0.0214%, nfe) (gnomAD).

What do computational predictors say about CFAP44 p.Phe1795Ser (c.5384T>C)?

AlphaMissense predicts likely pathogenic (score 0.6069) — an in-silico prediction, not a clinical call.

CFAP44 p.Phe1795Ser

c.5384T>C · VCV3352567

Uncertain significance No assertion criteria

Classification

Uncertain significance

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.6069 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0214%, nfe)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

CFAP44-related disorder

Computational evidence

Protein change
AlphaMissense	0.6069	likely pathogenic
REVEL	0.263	benign-leaning
SaProt	LLR -5.10	tolerated
⇒ AlphaMissense calls this damaging; REVEL and SaProt do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 2.4, phastCons 1
Regional constraint	o/e 0.93	unconstrained · MANE · 129 kb · p 0.0018 · regional, not allelic
Overall
CADD	25.4	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 0.0214% European (non-Finnish) · 246/1,146,932 alleles

Filtering AF 0.0192% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0184%

Overall 0.0174% 267/1,535,754 alleles · ultra-rare

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	0.024%	4,159
European (non-Finnish)grpmax	0.0214%	4,662
Remaining individualsnot grpmax-eligible	0.01%	9,993
Ashkenazi Jewishnot grpmax-eligible	0.00349%	28,654
Admixed American	0.00196%	50,988
African / African-American	0.00137%	72,966
South Asian	0.00119%	83,978

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Phe1795Ser
Coding: c.5384T>C
MANE Select: NM_001164496
Type: single nucleotide variant
Location: chr3:113291738 (GRCh38)
Gene constraint: LOEUF 0.697 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 74.87 · 1 PDB
Residue 1795: a UniProt-annotated variant site (in spgf20)

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

Disease context

CFAP44-related disorder

Similar variants

CFAP44 p.Arg977Ter Likely pathogenic ★ same condition
CFAP44 c.1570-5C>T Likely benign same condition
CFAP44 c.2716-8T>C Likely benign same condition
CFAP44 p.Ala1817= Likely benign same condition
CFAP44 p.Lys948= Likely benign same condition
CFAP44 p.Met820Val Benign same condition
CFAP44 p.Pro1254= Likely benign same condition
CFAP44 p.Leu873fs Likely pathogenic ★ 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-phe1795ser (accessed [today's date]).

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