Is CFAP44 p.Pro1254= (c.3762C>T) pathogenic?

CFAP44 p.Pro1254= (c.3762C>T) is classified Likely benign in CFAP44 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2020-02-24). Very rare (popmax 0.00235%, nfe); Associated with CFAP44-related disorder.

What condition is associated with CFAP44 p.Pro1254= (c.3762C>T)?

CFAP44 p.Pro1254= (c.3762C>T) is associated with CFAP44-related disorder (ClinVar).

How common is CFAP44 p.Pro1254= (c.3762C>T) in the general population?

CFAP44 p.Pro1254= (c.3762C>T) is very rare (popmax 0.00235%, nfe) (gnomAD).

CFAP44 p.Pro1254=

c.3762C>T · rs909097787 · VCV3051590

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00235%, nfe)

Conditions

CFAP44-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.3	GERP -4.4
Overall
CADD	0.142	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00235% European (non-Finnish) · 27/1,146,908 alleles

Filtering AF 0.00161% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00138%

Overall 0.00182% 28/1,537,054 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00235%	42,478
African / African-American	0.00137%	72,990

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.Pro1254=
Coding: c.3762C>T
MANE Select: NM_001164496
dbSNP: rs909097787
Type: single nucleotide variant
Location: chr3:113330522 (GRCh38)
Gene constraint: LOEUF 0.697 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 74.87 · 1 PDB
Residue 1254: 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 p.Phe1795Ser Uncertain significance ⚠ 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.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-pro1254 (accessed [today's date]).

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