Is KRIT1 p.Ala30= (c.90T>G) pathogenic?

KRIT1 p.Ala30= (c.90T>G) is classified Likely benign in KRIT1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-06-26). Very rare (popmax 0.000186%, nfe); Associated with Inborn genetic diseases.

What condition is associated with KRIT1 p.Ala30= (c.90T>G)?

KRIT1 p.Ala30= (c.90T>G) is associated with Inborn genetic diseases (ClinVar).

How common is KRIT1 p.Ala30= (c.90T>G) in the general population?

KRIT1 p.Ala30= (c.90T>G) is very rare (popmax 0.000186%, nfe) (gnomAD).

KRIT1 p.Ala30=

c.90T>G · VCV3535775

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.000186%, nfe)

Conditions

Inborn genetic diseases

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 1.4	GERP 0.12, phastCons 1
Overall
CADD	8.624	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000186% European (non-Finnish) · 2/1,076,608 alleles

Filtering AF 3.1e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.2e-05%

Overall 0.000133% 2/1,500,034 alleles · very rare exomes 2/1,347,734 · genomes 0/152,300 · joint denominator

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: KRIT1
Protein: p.Ala30=
Coding: c.90T>G
MANE Select: NM_194454
Type: single nucleotide variant
Location: chr7:92242046 (GRCh38)
Gene constraint: LOEUF 0.69 · pLI 0.11 (gnomAD)
Structure: AlphaFold pLDDT 83.01 · 15 PDB
Residue 30: an α-helix; the 'n-terminal domain similar to nudix hydrolase domain' region

Full KRIT1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

KRIT1 c.2025+3A>G Uncertain significance ★★ same condition
KRIT1 p.Arg167Cys Uncertain significance ★★ ⚠ same condition
KRIT1 p.Arg167His Uncertain significance ★★ ⚠ same condition
KRIT1 p.Arg179Gln Uncertain significance ★★ ⚠ same condition
KRIT1 p.Arg243Trp Uncertain significance ★★ ⚠ same condition
KRIT1 p.Arg306His Uncertain significance ★★ ⚠ same condition
KRIT1 p.Arg485Cys Uncertain significance ★★ ⚠ same condition
KRIT1 p.Asn403Ser Uncertain significance ★★ ⚠ 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/krit1-p-ala30 (accessed [today's date]).

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