Is IFT43 p.Lys54= (c.162A>G) pathogenic?

IFT43 p.Lys54= (c.162A>G) is classified Likely benign in IFT43 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-21). Ultra-rare (popmax 0.0132%, sas).

How common is IFT43 p.Lys54= (c.162A>G) in the general population?

IFT43 p.Lys54= (c.162A>G) is ultra-rare (popmax 0.0132%, sas) (gnomAD).

IFT43 p.Lys54=

c.162A>G · rs781025423 · VCV3011045

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0132%, sas)

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 -0.41	GERP -2.8, phastCons 0.001
Overall
CADD	0.377	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0132% South Asian · 12/91,068 alleles

Filtering AF 0.00751% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00593%

Overall 0.000806% 13/1,613,508 alleles · ultra-rare exomes 12/1,461,386 · genomes 1/152,122 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0132%	7,589
Remaining individualsnot grpmax-eligible	0.0016%	62,472

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: IFT43
Protein: p.Lys54=
Coding: c.162A>G
MANE Select: NM_001102564
dbSNP: rs781025423
Type: single nucleotide variant
Location: chr14:76022341 (GRCh38)
Gene constraint: LOEUF 1.282 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 64.09 · 3 PDB
Residue 54: the 'disordered' region

Full IFT43 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

IFT43 c.148-2A>C Likely pathogenic ★★ same type
IFT43 c.296-5698C>T Likely pathogenic ★★ same type
IFT43 c.296-5681A>G Uncertain significance ★★ same type
IFT43 c.296-5697G>A Uncertain significance ★★ same type
IFT43 c.444+5G>A Uncertain significance ★★ same type
IFT43 p.Ala162Thr Uncertain significance ★★ ⚠ same type
IFT43 p.Ala162Val Uncertain significance ★★ ⚠ same type
IFT43 p.Ala202Val 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/ift43-p-lys54 (accessed [today's date]).

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