Is CFAP44 p.Phe317Ser (c.950T>C) pathogenic?

CFAP44 p.Phe317Ser (c.950T>C) is classified Uncertain significance in CFAP44 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-05-10). AlphaMissense: likely pathogenic (0.9374); Ultra-rare (popmax 0.0107%, afr); Associated with Inborn genetic diseases.

What condition is associated with CFAP44 p.Phe317Ser (c.950T>C)?

CFAP44 p.Phe317Ser (c.950T>C) is associated with Inborn genetic diseases (ClinVar).

How common is CFAP44 p.Phe317Ser (c.950T>C) in the general population?

CFAP44 p.Phe317Ser (c.950T>C) is ultra-rare (popmax 0.0107%, afr) (gnomAD).

What do computational predictors say about CFAP44 p.Phe317Ser (c.950T>C)?

AlphaMissense predicts likely pathogenic (score 0.9374) — an in-silico prediction, not a clinical call.

CFAP44 p.Phe317Ser

c.950T>C · rs1341231955 · VCV3143496

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9374 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0107%, afr)

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.9374	likely pathogenic · top 4% in CFAP44
REVEL	0.574	indeterminate
SaProt	LLR -13.83	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 1.8, phastCons 1
Regional constraint	o/e 0.93	unconstrained · MANE · 129 kb · p 0.0018 · regional, not allelic
Overall
CADD	26.3	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0107% African / African-American · 8/74,930 alleles

Filtering AF 0.00528% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00381%

Overall 0.000929% 15/1,614,062 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0107%	9,366
Remaining individualsnot grpmax-eligible	0.0048%	20,829
East Asian	0.00223%	44,888
European (non-Finnish)	0.000254%	393,343

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.Phe317Ser
Coding: c.950T>C
MANE Select: NM_001164496
dbSNP: rs1341231955
Type: single nucleotide variant
Location: chr3:113406982 (GRCh38)
Gene constraint: LOEUF 0.697 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 74.87 · 1 PDB

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-phe317ser (accessed [today's date]).

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