Is HAL p.Gly197Ala (c.590G>C) pathogenic?

HAL p.Gly197Ala (c.590G>C) is classified Uncertain significance in HAL (ClinVar, Single submitter, 1 submitter; last evaluated 2018-01-12). AlphaMissense: ambiguous (0.3495); Ultra-rare (popmax 0.0984%, amr); Associated with histidinemia.

What condition is associated with HAL p.Gly197Ala (c.590G>C)?

HAL p.Gly197Ala (c.590G>C) is associated with histidinemia (ClinVar).

How common is HAL p.Gly197Ala (c.590G>C) in the general population?

HAL p.Gly197Ala (c.590G>C) is ultra-rare (popmax 0.0984%, amr) (gnomAD).

How is Histidinemia inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

What do computational predictors say about HAL p.Gly197Ala (c.590G>C)?

AlphaMissense predicts ambiguous (score 0.3495) — an in-silico prediction, not a clinical call.

HAL p.Gly197Ala

c.590G>C · rs541743724 · VCV881469

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3495 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0984%, amr)

Missense predictors

2/2 damaging

REVEL, SaProt · AlphaMissense indeterminate

Conditions

histidinemia

Computational evidence

Protein change
AlphaMissense	0.3495	ambiguous
REVEL	0.865	moderately pathogenic-leaning
SaProt	LLR -10.04	damaging
⇒ REVEL and SaProt both call this damaging; AlphaMissense is indeterminate.
Splicing
SpliceAI	Δ0.46	acceptor loss · deltas
Pangolin	Δ0.39	loss · gain 0.00 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 4.8	GERP 1.2, phastCons 1
Regional constraint	o/e 0.95	unconstrained · MANE · 22 kb · p 0.18 · regional, not allelic
Overall
CADD	25.6	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 0.0984% Admixed American · 59/59,980 alleles

Filtering AF 0.0783% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.071%

Overall 0.00384% 62/1,612,694 alleles · ultra-rare exomes 54/1,460,516 · genomes 8/152,178 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0984%	1,017
Remaining individualsnot grpmax-eligible	0.0032%	31,210
African / African-American	0.00134%	74,890

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: HAL
Protein: p.Gly197Ala
Coding: c.590G>C
MANE Select: NM_002108
dbSNP: rs541743724
Type: single nucleotide variant
Location: chr12:95992805 (GRCh38)
Gene constraint: LOEUF 1.213 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 90.83

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

Disease context

histidinemia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Histidinemia (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal
Prevalence: 1-9 / 100 000 (Sweden)

Similar variants

HAL p.Gly197Asp Uncertain significance ★ ⚠ same residue
HAL c.*392C>T Uncertain significance ★★ same condition
HAL p.Arg9Cys Uncertain significance ★★ ⚠ same condition
HAL p.Asn476Lys Uncertain significance ★★ ⚠ same condition
HAL p.Glu472Lys Uncertain significance ★★ ⚠ same condition
HAL p.Gly165Ser Uncertain significance ★★ ⚠ same condition
HAL p.Leu242Met Uncertain significance ★★ ⚠ same condition
HAL p.Phe485Leu 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/hal-p-gly197ala (accessed [today's date]).

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