Is CFAP44 p.Arg1845Ter (c.5533C>T) pathogenic?

CFAP44 p.Arg1845Ter (c.5533C>T) is classified Likely benign in CFAP44 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-12-31). Rare (popmax 0.708%, sas).

How common is CFAP44 p.Arg1845Ter (c.5533C>T) in the general population?

CFAP44 p.Arg1845Ter (c.5533C>T) is rare (popmax 0.708%, sas) (gnomAD).

CFAP44 p.Arg1845Ter

c.5533C>T · rs371164920 · VCV724581

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Rare

rare (popmax 0.708%, sas)

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	escapes	premature termination codon in the last exon (35 of 35) — the truncated protein is likely expressed. PVS1 input, not an applied code
REVEL	0.046	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.4	GERP 0.45, phastCons 0.057
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 0.708% South Asian · 595/84,046 alleles

Filtering AF 0.661% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.642%

Overall 0.0417% 641/1,537,194 alleles · rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.708%	141
Remaining individualsnot grpmax-eligible	0.0416%	2,401
Middle Eastern	0.0334%	2,994
Admixed American	0.00588%	16,997
African / African-American	0.00547%	18,285
Finnishnot grpmax-eligible	0.00439%	22,801
East Asian	0.00244%	40,924
European (non-Finnish)	0.000785%	127,434

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.Arg1845Ter
Coding: c.5533C>T
MANE Select: NM_001164496
dbSNP: rs371164920
Type: single nucleotide variant
Location: chr3:113291589 (GRCh38)
Gene constraint: LOEUF 0.697 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 74.87 · 1 PDB
Residue 1845: 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.Arg1845= Likely 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-arg1845ter (accessed [today's date]).

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