Is CFAP47 p.Thr768Ser (c.2302A>T) pathogenic?

CFAP47 p.Thr768Ser (c.2302A>T) is classified Likely benign in CFAP47 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2022-05-26). AlphaMissense: likely benign (0.1099); Rare (popmax 0.249%, nfe); Associated with CFAP47-related disorder.

What condition is associated with CFAP47 p.Thr768Ser (c.2302A>T)?

CFAP47 p.Thr768Ser (c.2302A>T) is associated with CFAP47-related disorder (ClinVar).

How common is CFAP47 p.Thr768Ser (c.2302A>T) in the general population?

CFAP47 p.Thr768Ser (c.2302A>T) is rare (popmax 0.249%, nfe) (gnomAD).

What do computational predictors say about CFAP47 p.Thr768Ser (c.2302A>T)?

AlphaMissense predicts likely benign (score 0.1099) — an in-silico prediction, not a clinical call.

CFAP47 p.Thr768Ser

c.2302A>T · rs140595411 · VCV3043436

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1099 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.249%, nfe)

Missense predictors

0/2 damaging

AlphaMissense, REVEL

Conditions

CFAP47-related disorder

Computational evidence

Protein change
AlphaMissense	0.1099	likely benign
REVEL	0.02	moderately benign-leaning
⇒ AlphaMissense and REVEL both call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.2	GERP 2.2, phastCons 0.98
Regional constraint	o/e 1.10	unconstrained · MANE · 465 kb · p 2.3e-05 · regional, not allelic
Overall
CADD	1.953	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 0.249% European (non-Finnish) · 2,207/885,398 alleles

Filtering AF 0.241% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.237%

Overall 0.208% 2,494/1,197,889 alleles · rare

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.516%	194
European (non-Finnish)grpmax	0.249%	401
Remaining individualsnot grpmax-eligible	0.167%	597
Finnishnot grpmax-eligible	0.0863%	1,159
Admixed American	0.0859%	1,164
Middle Eastern	0.0697%	1,435
African / African-American	0.0229%	4,371

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: CFAP47
Protein: p.Thr768Ser
Coding: c.2302A>T
MANE Select: NM_001304548
dbSNP: rs140595411
Type: single nucleotide variant
Location: chrX:35975194 (GRCh38)

Full CFAP47 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

CFAP47-related disorder

Similar variants

CFAP47 p.Pro2938Leu Uncertain significance ★ ⚠ same condition
CFAP47 p.Arg870Gln Likely benign same condition
CFAP47 p.Asn2174Asp Likely benign same condition
CFAP47 p.Asn2541Ser Likely benign same condition
CFAP47 p.Asp1458Val Likely benign same condition
CFAP47 p.Gln4Ter Likely benign same condition
CFAP47 p.Ile1321Val Likely benign same condition
CFAP47 p.Ile2102Val Likely benign 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/cfap47-p-thr768ser (accessed [today's date]).

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