Is CFAP44 p.Gln87Ter (c.259C>T) pathogenic?

CFAP44 p.Gln87Ter (c.259C>T) is classified Pathogenic in CFAP44 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-06-28). Rare (popmax 0.156%, afr).

How common is CFAP44 p.Gln87Ter (c.259C>T) in the general population?

CFAP44 p.Gln87Ter (c.259C>T) is rare (popmax 0.156%, afr) (gnomAD).

CFAP44 p.Gln87Ter

c.259C>T · rs142299289 · VCV2058075

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Rare

rare (popmax 0.156%, afr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function
NMD	predicted	premature termination codon in exon 4 of 35
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.2	GERP 0.77, phastCons 1
Overall
CADD	35.0	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.156% African / African-American · 117/74,830 alleles

Filtering AF 0.133% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.125%

Overall 0.0075% 121/1,612,806 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.156%	640
Remaining individualsnot grpmax-eligible	0.00481%	20,797
Admixed American	0.00168%	59,664

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.Gln87Ter
Coding: c.259C>T
MANE Select: NM_001164496
dbSNP: rs142299289
Type: single nucleotide variant
Location: chr3:113426272 (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.Gln87Leu Benign ★★ 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-gln87ter (accessed [today's date]).

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