Is INTS1 p.Ser51= (c.153C>T) pathogenic?

INTS1 p.Ser51= (c.153C>T) is classified Likely benign in INTS1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-03-01). Ultra-rare (popmax 0.011%, sas).

How common is INTS1 p.Ser51= (c.153C>T) in the general population?

INTS1 p.Ser51= (c.153C>T) is ultra-rare (popmax 0.011%, sas) (gnomAD).

INTS1 p.Ser51=

c.153C>T · rs371226645 · VCV737204

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.011%, 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 -10	GERP -4.4
Overall
CADD	2.41	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.011% South Asian · 10/90,972 alleles

Filtering AF 0.00938% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00881%

Overall 0.0106% 171/1,610,578 alleles · ultra-rare exomes 156/1,458,376 · genomes 15/152,202 · joint denominator

Ancestry group	Frequency	1 in
Remaining individualsnot grpmax-eligible	0.0241%	4,155
South Asiangrpmax	0.011%	9,097
European (non-Finnish)	0.011%	9,128
Finnishnot grpmax-eligible	0.00942%	10,611
Admixed American	0.00835%	11,978
African / African-American	0.00801%	12,481

Remaining individuals 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: INTS1
Protein: p.Ser51=
Coding: c.153C>T
MANE Select: NM_001080453
dbSNP: rs371226645
Type: single nucleotide variant
Location: chr7:1503097 (GRCh38)
Gene constraint: LOEUF 0.785 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 75.49 · 8 PDB
Residue 51: the 'disordered' region

Full INTS1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

INTS1 c.3430-2A>C Likely pathogenic ★★ same type
INTS1 p.Arg101Ter Likely pathogenic ★★ same type
INTS1 p.Glu182Ter Likely pathogenic ★★ same type
INTS1 c.1283+5G>A Uncertain significance ★★ same type
INTS1 c.2977-5C>T Uncertain significance ★★ same type
INTS1 p.Ala1112Val Uncertain significance ★★ ⚠ same type
INTS1 p.Ala1505Val Uncertain significance ★★ ⚠ same type
INTS1 p.Ala1854Val 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/ints1-p-ser51 (accessed [today's date]).

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