Is CFAP144 p.Ile100Val (c.298A>G) pathogenic?

CFAP144 p.Ile100Val (c.298A>G) is classified Conflicting classifications of pathogenicity in CFAP144 (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2022-08-18). AlphaMissense: likely benign (0.0601); Rare (popmax 0.122%, nfe).

How common is CFAP144 p.Ile100Val (c.298A>G) in the general population?

CFAP144 p.Ile100Val (c.298A>G) is rare (popmax 0.122%, nfe) (gnomAD).

What do computational predictors say about CFAP144 p.Ile100Val (c.298A>G)?

AlphaMissense predicts likely benign (score 0.0601) — an in-silico prediction, not a clinical call.

CFAP144 p.Ile100Val

c.298A>G · rs201490932 · VCV1710363

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.0601 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.122%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0601	likely benign
REVEL	0.016	strongly benign-leaning
SaProt	LLR -7.29	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · A>T here scores Δ0.35 · evaluated, not missing
Constraint at this position
Conservation	phyloP 0.88	GERP -1.3, phastCons 1
Regional constraint	o/e 0.91	unconstrained · MANE · 8,358 bp · p 0.24 · regional, not allelic
Overall
CADD	7.577	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 0.122% European (non-Finnish) · 1,439/1,179,696 alleles

Filtering AF 0.117% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.115%

Overall 0.0925% 1,493/1,613,608 alleles · rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.122%	820
Remaining individualsnot grpmax-eligible	0.0416%	2,402
African / African-American	0.0307%	3,256
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,608
Admixed American	0.00333%	29,999
Finnishnot grpmax-eligible	0.00313%	32,000

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: CFAP144
Protein: p.Ile100Val
Coding: c.298A>G
MANE Select: NM_001101376
dbSNP: rs201490932
Type: single nucleotide variant
Location: chr1:43156206 (GRCh38)
Structure: AlphaFold pLDDT 79.41 · 2 PDB

Full CFAP144 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CFAP144 p.Arg104Cys Uncertain significance ★ ⚠ same type
CFAP144 p.Asp130Gly Uncertain significance ★ ⚠ same type
CFAP144 p.Asp57Gly Uncertain significance ★ ⚠ same type
CFAP144 p.Asp64Asn Uncertain significance ★ ⚠ same type
CFAP144 p.Glu60Gly Uncertain significance ★ ⚠ same type
CFAP144 p.Gly129Val Uncertain significance ★ ⚠ same type
CFAP144 p.His56Tyr Uncertain significance ★ ⚠ same type
CFAP144 p.Lys26Arg Uncertain significance ★ ⚠ 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/cfap144-p-ile100val (accessed [today's date]).

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